Query: Emergence in Solid State Physics and Biology

Candidate papers:

abstract: There has been much controversy over weak and strong emergence in physics and biology. As pointed out by Phil Anderson in many papers, the existence of broken symmetries is the key to emergence of properties in much of solid state physics. By carefully distinguishing between dfferent types of symmetry breaking and tracing the relation between broken symmetries at micro and macro scales, I demonstrate that the emergence of the properties of semiconductors is a case of strong emergence. This is due to the existence of quasiparticles such as phonons. Furthermore time dependent potentials enable downward causation as in the case of digital computers. Additionally I show that the processes of evolutionary emergence of living systems is also a case of strong emergence, as is the emergence of properties of life out of the underlying physics. A useful result emerges: standard physics theories and the emergent theories arising out of them are all effective theories that are equally valid
author_names: George F R Ellis
title: Emergence in Solid State Physics and Biology
year: 2020

abstract: The causal closure of physics is usually discussed in a context free way. Here I discuss it in the context of engineering systems and biology, where strong emergence takes place due to a combination of upwards emergence and downwards causation (Ellis, Emergence in Solid State Physics and Biology, 2020, arXiv:2004.13591) Firstly, I show that causal closure is strictly limited in terms of spatial interactions because these are cases that are of necessity strongly interacting with the environment. Effective Spatial Closure holds ceteris parabus, and can be violated by Black Swan Events. Secondly, I show that causal closure in the hierarchy of emergence is a strictly interlevel affair, and in the cases of engineering and biology encompasses all levels from the social level to the particle physics level. However Effective Causal Closure can usefully be defined for a restricted set of levels, and one can experimentally determine Effective Theories that hold at each level. This does not however imply those effective theories are causally complete by themselves. In particular, the particle physics level is not causally complete by itself in the contexts of solid state physics (because of interlevel wave particle duality) digital computers (where algorithms determine outcomes) or biology (because of time dependent constraints) Furthermore Inextricably Intertwined Levels occur in all these contexts.
author_names: George F R Ellis
title: The Causal Closure of Physics in Real World Contexts
venue: Foundations of physics
year: 2020

abstract: During the last 40 years, with close collaboration between the physicist and medical staff, instrumentation in medicine has advanced enormously. The possibility of such advance depended on two major developments in basic science. The first was the emergence of electronics. Until the early 1940s the word electronics was scarcely known. Now this has become a vast field of technological progress. The second was the impact of solid state physics, which made its mark at about the same time. The developments that have taken place during the succeeding decades have derived very largely from these two new sources. The developments may be divided broadly into four stages, each corresponding roughly to one of the four decades considered. These stages involve valves, transistors, integrated circuits and instrumentation systems.
author_names: Frank T Farmer
title: 40 years of instrumentation for medicine.
venue: Physics in medicine and biology
year: 1984

abstract: We study the S=1/2 Heisenberg (J) model on the two dimensional square lattice in the presence of additional higher order spin interactions (Q) which lead to a valence bond solid (VBS) ground state. Using quantum Monte Carlo simulations, we analyze the thermal VBS transition. We find continuously varying exponents, with the correlation length exponent "nu" close to the Ising value for large Q/J and diverging when Q/J approaches the quantum critical point (the critical temperature Tc 0) This is in accord with the theory of deconfined quantum critical points, which predicts that the transition should approach a Kosterlitz Thouless (KT) fixed point when Tc 0+ (while the transition versus Q/J for T=0 is in a different class) We find explicit evidence for KT physics by studying the emergence of U(1) symmetry of the order parameter at T=T_c when Tc 0.
author_names: Songbo Jin

Anders W Sandvik
title: Thermal valence bond solid transition of quantum spins in two dimensions
year: 2013

abstract: Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India, Biochemistry and Structural Biology, Lund University, Box 117, Lund, 22100, Sweden, Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE 751 24 Uppsala, Sweden, and Hockmeyer Hall of Structural Biology, Purdue University, West Lafayette, IN 47907 1971, USA. *Correspondence e mail: anders@liljas.net
author_names: K K Kannan

Anders Liljas

Lars Liljas

Seved Lofgren

Michael G Rossmann

Torsten Unge
title: Bror Erik Strandberg (1930 2018)
venue: Acta crystallographica. Section D, Structural biology
year: 2018

abstract: The work is devoted to the development of a smart lighting system that is able to change correlated colour temperature and consists of tunable 4 components RGBW clusters controlled via three channels. It is shown that fixing a ratio between the intensities of white and red LEDs at a level of 100:9 enables obtaining high values of colour rendering in a wide range of correlated colour temperatures. The control of 3 from 4 channels simplifies the system. The influence of the red LED on CRI and luminous efficiency is analysed. Light is an important part of human life. Numerous studies on lighting and its influence on our health, as well as the effect on a psychoemotional state and indoor comfort have been done [1/2] Due to the long evolutionary process of human adaptation to natural conditions and the dynamics of lighting changes, natural light is the most comfortable for us. Therefore, an important task in creating light sources is the reproduction of natural daylight parameters, both in terms of the dynamics of intensity and spectral changes providing high color rendering. The rapid development of solid state light sources has led to the emergence of functionally new smart lighting systems (SLS) Using several types of LEDs with different spectral power distributions (SPDs) it is possible to get a lighting system being able to change smoothly SPD of the resulting light characterised by correlated colour temperature (CCT) color rendering, and intensity. This enables us to create a comfortable lighting environment. There are many approaches used for color tunable LED systems which differ in quantity of LEDs (two and more) and methods of colour mixing [3/4] The fact is that when two or three LEDs (control channels) are involved, there is a unique opportunity to determine how LEDs contribute to obtaining the resulting white light. The problem in this case is only choosing the needed LEDs. However, when an SLS includes four and more coloured LEDs, determining the LEDs contribution is not unique. Therefore, further development of algorithms is needed for such a type of SLS requiring additional conditions. The purpose of this letter is to report on an optimisation method determining the contributions of red, green, blue, and white (RGBW) LEDs in an SLS, which is controlled E mail: sergiy.valyukh@liu.se via three channels to achieve high color rendering in a wide CCT range. Colour rendering is analysed in terms of fidelity index Rf [5] proposed for scientific application in CIE 224:2017, as well as widely accepted color rendering index (CRI) [6] In addition to high color rendering at one or another CCT, the advantage of an SLS is its simple controlling principle. There are two alternatives to simplify the control principle of an SLS: reducing the number of different coloured LEDs included in an SLS and optimizing the use of the existing set of LEDs. The first option may have a negative effect on resulting light SPDs or require the use of non typical phosphor based LEDs with a wide emission band. Therefore, let us consider the second alternative. A RGBW SLS consists of three dedicated coloured LEDs and a phosphor based white (W) LED. Since the CRI values of typical W LEDs are higher than of the white light being generated by three coloured LEDs, it is reasonable to form the resulting light with a significant contribution of the W LED. In this case, the functionality of the coloured LEDs is restricted to the correction of the resulting white light chromaticity coordinates in accordance with CCT. Analysis of the influence of the W LED on the parameters of the resulting light of a RGBW SLS shows that a warm W LED with a CCT of about 3000K and CRI of about 80 is the most effective for obtaining high CRI in a wide CCT range [7] In order to get the resulting RGBW light having CCT above 3000K by using such a W LED, it is necessary to modify its SPD with coloured LEDs, by shifting the chromaticity coordinates in the blue green region of the CIE diagram. Because of this, the contribution of green (G) and blue (B) LEDs to the resulting spectrum is higher than that of the red (R) LED one. Like in the two white LEDs systems [4] the manipulation of the light spectrum in the RGBW SLS can be done owing to the ratio change between the two parts when the first one contains mostly short wavelengths and the other affects long wavelengths. The ratio between these parts correlates with the contributions of B and G LEDs on the one hand and R and W LEDs on the other Color temperature tunable RGBW clusters with 3 control channels Daria Kalustova, Vasyl Kornaga, Andrii Rybalochka, Ying Jie Yu, Sergiy Valyukh 1 V. Lashkaryov Institute of Semiconductor Physics NAS of Ukraine, Kyiv, Ukraine, 2 Department of Precision Mechanical Engineering, Shanghai University, China, 3 Department of Physics, Chemistry and Biology, Linkoping University, Linkoping, Sweden Received December 23, 2019; accepted March 27, 2020; published March 31, 2020 doi: 10.4302/plp.v12i1.968 PHOTONICS LETTERS OF POLAND, VOL. 12 (1) 10 12 (2020) http:/www.photonics.pl/PLP (c) 2020 Photonics Society of Poland 11 hand. The study on intensity contributions of R and W LEDs to the resulting light showed that these contributions are nearly proportional to each other when it is necessary to obtain high CRI in a wide CCT range. If so, we can determine the optimal ratio between the contributions of R and W LEDs, and after that fix their brightnesses ratio and control both LEDs via one channel. This will optimize and simplify the control system of an SLS. Moreover, the fixed ratio of brightness between R and W LEDs resolves the problem how to determine the contributions of the B and G LEDs to obtaining a point on the Planck curve. Thus, the further objective of the work is to determine the optimal ratio between the brightnesses of two LEDs (W:R) when the resulting RGBW light has high Rf and CRI in a wide CCT range. In order to investigate the problem, two SLSs were studied. They had three identical LEDs: W (2985K, CRI 82) blue (461 nm) and green (525 nm) LEDs, but a different red component. The first one (RGBW SLS) used R LED with a peak wavelength of 625 nm, and the second SLS (dRGBW) used deep red (dR) LED with a peak wavelength of 662 nm. The SPDs of the resulting light having the chromaticity coordinates coincident with the Planck curve were simulated for different fixed ratios between the brightness of the R and W LEDs for an RGBW SLS, as well as the ratio between the brightness of the dR and W LEDs for dRGBW. The resulting light parameters were calculated from these SPDs. The contributions of the R and dR LEDs varied from 1% to 15% with respect to the contribution of the W LED, the step was 1% The CCT of the resulting white light therewith changes in the range of 2900 7000K with the Duv (Delta u,v) parameter less than 0.0005. A further increase in R contribution, as well as that of dR, above 15% is unreasonable. The obtained results were analysed in terms of Rf, CRI and CCT. Some of the curves that enable one to judge the influence of the ratio R/W, as well as dR/W, on Rf and CRI are presented in Fig. 1 and Fig. 2. The curves are labelled with corresponding to the R and dR LEDs contributions with respect to the W LED. According to Fig. 1a, the maximums of Rf for different R LED contributions reach 88 94 in the full CCT range. The obtained dependences show that when the R LED brightness is fixed at a level of 6 9% of the W LED brightness, the yield Rf values can be above 90 in the CCT range of 2900 5000K, but the 9% of brightness gives higher Rf values in general. At the same time, for all these R LED brightnesses, the yield CRI values can be above 91 in the full CCT range (Fig. 2) But since most of the daytime natural daylighting CCT is about 5000 6500 K, in terms of maximum CRI values it is reasonable to choose the R LED brightness at the level of 6% when it gives higher CRI values in this CCT range. Fig. 1. Fidelity Index Rf vs. CCT for RGBW (a) and dRGBW (b) SLSs at different red component contributions. For the dRGBW SLS, Fig. 1b demonstrates a different curve behaviour compared to the previous case. The contribution of dR LED affects Rf and CRI more than that of R LED. A significant decrease is observed of Rf and CRI at high CCTs with an increase in the dR LED brightness contribution from 3% to 13% The maximums of Rf reach 88 95 and the maximums of CRI reach 94 98. Adhering to the similar principle as with the R LED, it is reasonable to fix the dR LED brightness at the level of 3% of the W LED both in terms of Rf and CRI values. It allows us to obtain the Rf values over 90 in the CCT range of 2900 5500K and CRI values over 92 in the full CCT range (Fig. 2) Fig. 2. CRI vs. CCT for RGBW (solid curves) and dRGBW (dashed curves) SLSs at different red component contributions. Thus, the RGBW lighting system has Rf values 87 93 and CRI values 91 97 in the CCT range 2900 7000K at a fixed ratio R/W equal to 0.09 (9% of the R LED) A ratio dR/W equal to 0.03 (3% the dR LED) makes it possible to obtain Rf values 88 93 and CRI values 92 98 in the same CCT range for the dRGBW SLS. a)
author_names: Daria Kalustova

Vasyl Kornaga

Andrii Rybalochka

Yingjie Yu

Sergiy Valyukh
title: Colour temperature tunable RGBW clusters with 3 control channels
year: 2020

abstract: It is difficult to determine when the area termed 'Supramolecular Chemistry' started and thus what anniversary there really is. Where from? The term itself, which is now widely accepted and has deeply permeated chemical literature, was introduced by this author in two publications in 1978 in order to define, consolidate and generalize the areas of crown ether chemistry, host guest chemistry and the chemistry of molecular recognition, thus allowing for the emergence of the concepts and perspectives offered. However, much earlier and before 1967, fifty years ago, entities formed by the binding together of molecules, known as molecular complexes, had already been investigated here and there, as well as macrocyclic complexes of natural (such as cation binding antibiotics) and synthetic types, until the forest was seen beyond a collection of trees. As anniversaries go, 2017 also marks the 30 anniversary of the 1987 Nobel Prize in Chemistry, which recognized the three areas of crown ether, host guest and molecular recognition chemistries already mentioned above. Supramolecular chemistry has been defined as 'chemistry beyond the molecule' as it aims at designing and implementing functional chemical systems based on molecular components held together by noncovalent intermolecular forces. It has over the last half a century grown into a major field and has fuelled numerous developments at the interfaces with biology and physics; from basic knowledge to applications, from noncovalent interactions to drug design, and from materials and polymers to solid state engineering. It thus gave rise to the emergence and establishment of supramolecular science and technology, as a broad multidisciplinary and interdisciplinary domain providing a highly fertile ground for the creativity of scientists from all origins. Arguably the major conceptual contribution of supramolecular chemistry to chemistry has been to extol and implement the notion of chemical information, as it operates in molecular recognition processes, being stored at the molecular level in the framework of molecules and implemented at the supramolecular level in the buildup (synthesis! of discrete or extended assemblies of chemical objects. It forms the basis of the universal principle of selforganisation, the feature that on the wide scene is the driving force of the development of complex matter in our universe. Where to is supramolecular chemistry then heading? Of course, many directions for future development will be found or may be extrapolated from the set of contributions collected in the present special publication. A feature of particular interest is the dynamic character of supramolecular chemistry, its ability to explore a multitude of combinations by exchange and selection of molecular components for the generation of a given supramolecular entity from a diverse collection of building blocks until the 'best' constitution (thermodynamically and kinetically) is attained. The introduction of such dynamic character into molecular chemistry and the exploration of the perspectives thus opened have given rise to an independently developing field, dynamic covalent chemistry, where the molecular entity contains covalent bonds that may form and break reversibility, so as to allow a continuous change in constitution by reorganization and exchange of building blocks. Thus, supramolecular chemistry has also been fertilizing molecular chemistry and has led to the emergence of an adaptive chemistry, which plays on constitutional diversity in dynamic chemical systems at both the molecular and supramolecular levels to allow for variation and selection in a selforganisation process to achieve adaptation. Along the path from 'Where from? to 'Where to? supramolecular chemistry has played and is playing a major role in the development of chemistry. The breadth and depth of its scope is witnessed and illustrated by the wide range and very numerous publications, reviews and books that have sprung up in the past fifty years. The collection of papers by a select group of major players in the field gathered in the present special issue of Chemical Society Reviews illustrates in a most convincing way the achievements and the vitality of supramolecular chemistry. This author has written extensively about the field, describing its core realizations, its Institut de Science et d'Ingenierie Supramoleculaires (ISIS) University of Strasbourg, 8 Rue Gaspard Monge, Strasbourg 67000, France. E mail: lehn@unistra.fr DOI: 10.1039/c7cs00115k
author_names: Jean-Marie Lehn
title: Supramolecular chemistry: Where from? Where to?
venue: Chemical Society reviews
year: 2017

abstract: Part II of this review elaborates a hypothesis presented in Part I (2003 Liq. Cryst. 30, 541) and earlier publications. This hypothesis proposes that specified naturally occurring substances in the aqueous lyotropic mesophase of the liquid crystalline state of matter possess the ability to replicate, polymerize spontaneously and engage in further transitions to form ordered two and three dimensional layered, cubic, helical and spherulitic structures resembling those described geochemically, and observed experimentally in elementary forms of living substance. This ability uses energy originating in the kinetics of particles showing Brownian movements, spin and tensions at liquid liquid and solid liquid interfaces. Energy is derived also from chemiosmosis, phosphorylation, negative entropy and bonding by covalent and electro weak forces to build macromolecules in ordered sequences of lipids, peptides and nucleic acids. These can polymerize to form glyco and lipo proteins, polynucleotides, anabolic and catalytic enzymes, plausibly and causally associated with the morphogenesis, metabolism and replication of protista, plankton and other primitive forms of life observed in prebiotic pools and surfaces of the cooling litho hydrosphere of planet earth. Interactions in these ecological niches would undoubtedly promote biochemical evolution compatible with self organization of diversified living processes. These phenomena reveal plausible, natural mechanisms for formation of bilayer membranes with ionic channels, and other ordered structures providing spaces in which oxidative reactions and syntheses may proceed. All of this can be linked causally to early steps in animation of matter in accordance with laws governing particle physics and chemistry, templates and the general logic of molecular memories expressed in polynucleotides and proteins. Phenomena indicative of transfer of information, cellular organization, metabolism and transmission of neural signals are identifiable additionally as mechanisms for diversification and evolution. There are, however, credibility gaps in trying to extend this reasoning to sexual reproduction, speciation, competitive survival and ontogeny in the higher plants and metazoa. Various probabilities are discussed in statistical and physico chemical terms. It is suggested that these could justify the hypothesis in so far as natural processes are sufficient to engender conditions for emergence of primitive life and Darwinian evolution in eco niches of terrestrial space and measurable time. But there are also, in the unique utilization of energy, exploitation of advantages and adaptive capabilities of organisms at all levels to changing environmental stresses, many indications of teleonomic forces operating in ways for which there is no explanation in accordance with the laws of physical or chemical processes. This might be because understanding of particle physics and wave mechanics is insufficiently deployed in molecular biology, or because the laws of physics are scientifically incomplete in this respect.
author_names: Gordon Thallon Stewart
title: Liquid crystals in biology II. Origins and processes of life
year: 2004

abstract: The brain is an intricately structured organ responsible for the rich emergent dynamics that support the complex cognitive functions we enjoy as humans. With around 1011 neurons and 1015 synapses, understanding how the human brain works has proven to be a daunting endeavor, requiring concerted collaboration across traditional disciplinary boundaries. In some cases, that collaboration has occurred between experimentalists and technicians, who offer new physical tools to measure and manipulate neural function. In other contexts, that collaboration has occurred between experimentalists and theorists, who offer new conceptual tools to explain existing data and inform new directions for empirical research. In this chapter, we offer an example of the latter. Specifically, we focus on the simple but powerful framework of linear systems theory as a useful tool both for capturing biophysically relevant parameters of neural activity and connectivity, and for analytical and numerical study. We begin with a brief overview of state space representations and linearization of neural models for non linear dynamical systems. We then derive core concepts in the theory of linear systems such as the impulse and controlled responses to external stimuli, achieving desired state transitions, controllability, and minimum energy control. Afterwards, we discuss recent advances in the application of linear systems theory to structural and functional brain data across multiple spatial and temporal scales, along with methodological considerations and limitations. We close with a brief discussion of open frontiers and our vision for the future. Jason Z. Kim Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA e mail: jinsu1@seas.upenn.edu Danielle S. Bassett Departments of Bioengineering, Electrical Systems Engineering, Physics Astronomy, Neurology, Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA e mail: dsb@seas.upenn.edu 1 ar X iv :1 90 2. 03 30 9v 1 qbi o. N C 8 F eb 2 01 9 2 Jason Z. Kim and Danielle S. Bassett 1 Emergence in the Structure and Function of Complex Systems In the observable world, some of the most beautiful and most puzzling phenomena arise in physical and biological systems characterized by heterogeneous interactions between constituent elements. For example inmaterials physics, heterogeneous interactions between particles in granular matter (such as a sand pile) constrain whether the matter acts as a liquid (flowing with gravity) or a solid (supporting load bearing) [1, 2] In sociology, heterogeneous interactions between humans in a society are thought to be responsible for surges in online activity, peaks in book sales, traffic jams, and correlated spikes in demand for emergency services [3] In biology, heterogeneous interactions between computational units in the brain are thought to support a divergence of the correlation length, an anomalous scaling of correlation fluctuations, and the manifestation of mesoscale structure in patterns of functional coupling between units, all features that allow for a diversity of dynamics underlying a diversity of cognitive functions [4, 5] The feature of these systems that often drives our fascination is the capacity for heterogeneous interactions to produce suprising dynamics, in the form of drastic state transitions, spikes of collective activity, and multiple accessible dynamical regimes. Because element element interactions are heterogeneous in such systems, traditional approaches from statistical mechanics such as continuum models and mean field approximations fail to offer satisfying explanations for system function. There exists a critical need to develop alternative approaches to understand how interactions map to emergent behavior. The need is particularly salient in the context of neural systems, where such an understanding could directly inform models of neurological disease and psychiatric disorders [6, 7] Moreover, gaining such an understanding is a prerequisite for the well reasoned development of interventions [8] whether in the form of brain stimulation [9, 10] pharmacological agents [11, 12] or other therapies [13] Technically, such interventions in systems characterized by heterogeneous interactions can be parsimoniously considered as forms of network control, thus motivating extensive recent interest in the utility of network control theory for neural systems [8] Despite the generic importance of understanding how interactions map to emergent properties, and the specific importance of understanding that mapping in the human brain, progress towards that understanding has remained surprisingly slow. Some efforts have sought to develop detailed multiscale computational models [14] Yet such efforts are faced with the ever present quandary that, in point of fact, "The best material model of a cat is another, or preferably the same, cat" [15] Detailed models are difficult to construct, intractable to analytic approaches, require extensive time to simulate, contain parameters that are frequently underconstrained by experimental data, and in the end produce dynamics that are themselves difficult to understand or to explain from any specific choices in the model. In contrast, approaches from physics consider natural phenomena as if dynamics at macroscopic length scales were almost independent of the underlying, shorter length scale details [16] A hallmark of effective physical theories is a marked compression of the full parameter space into a few governing variables that are sufficient to describe Linear Dynamics Control of Brain Networks 3 the observables of interest at the scale of interest. Interestingly, recent theoretical work demonstrates that such simple models are the natural culmination of processes maximizing the information learned from finite data [17] Here we embrace simplicity by considering the utility of linear systems theory for the understanding and control of neural systems comprised of computational units coupled by heterogeneous interactions. We begin by placing our remarks within the context of quantitative dynamical models of neurons and their interactions, as well as the spatial and temporal considerations inherent in choosing such models. We will then turn to a discussion of approximations to those dynamical models, the incorporation of exogeneous control input, and model linearization. Our treatment then naturally brings us to a discussion of the theory of linear systems, as well as their response to perturbative impulses, and to explicit control strategies. We lay out the formalism for probing state transitions, controllabilty, and the minumum control energy needed for a given state transition. After completing our formal treatment, we discuss the application of linear systems theory to neural systems, and efforts to map network architecture to control properties. We close with a description of several particularly pertinent methodological considerations and limitations, before outlining emerging frontiers. 2 Quantitative Dynamical Models of Neural Systems Interactions Historically,many neural behaviors andmechanisms have been successfullymodeled quantitatively. Here we briefly describe several illustrative examples of such models. The classic fundamental biophysical model of a single neuron (Fig. 1, left) was developed by Alan Hodgkin and Andrew Huxley in 1952 (see [18] for details) The model is now known as theHodgkin Huxleymodel. It treats a segment of a neuron as an electrical circuit, where the membrane (capacitor) and voltage gated ion channels (resistors) are parallel circuit elements. The time evolution of membrane voltage, Vm, between the inside and the outside of the neuron is given by Cm U Vm(t) gKn(t)(VK Vm) gNam(t)h(t)(VNa Vm) gl(Vl Vm) I(t) where Cm is the membrane capacitance, gK, gNa, gl are maximum ion conductances for potassium, sodium, and passive leaking ions, and I is an external stimulus current, all per unit area. In addition,VK,VNa,Vl represent the reversal potential of these ions. The variables n,m, h vary between 0 and 1, and model the ion channel gate kinetics to determine the fraction of open sodium (m, h) and potassium (n) channels U n(t) an(Vm(t)(1 n(t) bn(Vm(t))n(t) U m(t) am(Vm(t)(1 m(t) bm(Vm(t))m(t) U h(t) ah(Vm(t)(1 h(t) bh(Vm(t))h(t) 4 Jason Z. Kim and Danielle S. Bassett where the functions ai(Vm) and bi(Vm) are empirically determined. These segments are then spatially connected together, such that the propagation of an action potential across a neuron is modeled by a set of partial differential equations. Due to the biophysical realism of variables and parameters, this model can make powerful and accurate predictions of neuron activity in different environments and stimulation regimes [19, 20, 21] Simplified versions of this model, such as the FitzHughNagumo model [22] can also produce many of the same neuronal dynamics. Fig. 1 Schematic of neural models and controlling perturbations at different scales. Here, the Hodgkin Huxley model describes the biophysical behavior of single neurons (left) that may be excitatory (blue) or inhibitory (gray) The artificial neuron models describe the simplified weighted connections and binary states of many neurons (center) The Wilson Cowan model describes the activity of large neural populations in a region (right) or in a cortical column by modeling the excitatory and inhibitory connections of each population. In each case, a controlling perturbation (yellow) can affect the neural system at different scales. However, many complex behaviors of neural systems arise from interactions between multiple neurons. With four variables (membrane voltage, gates) and even more parameters to model the behavior of a single neuron, the space of models to explore interacting neurons quickly becomes intractable to both analytical and numerical interrogation.
author_names: Jason Z Kim

Danielle S Bassett
title: Linear Dynamics&Control of Brain Networks
year: 2019

abstract: Combined optical trapping (OT) and single molecule fluorescence (SMF) find use in single molecule biology [1] SMF experiments involve labeling the molecule of interest with a small number of fluorophores. Hence, minimizing background fluorescence is essential to ensure sufficient signal to noise ratio. Total internal reflection fluorescence (TIRF) localizes the excitation to within approximately 150 nm layer from the surface, effectively restricting the background [2,3] Since OT experiments employ dielectric beads in the micrometer size range, additional optically transparent step like surface structures are needed to raise the excitation volume close to the trapped molecule [3].We implemented TIRF imaging into an existing optical tweezer instrument [4] A diode pumped solid state laser excites fluorescence (Coherent Sapphire 50 mW, 488 nm) Video capture is realized with an EMCCD camera (Andor iXon DU 897) A fluorescence emission filter (Chroma HQ535/30m) blocks the wavelengths corresponding to the trapping and detection lasers. TIRF is achieved with a high NA objective (Nikon CFI Plan Apo 100X TIRF) Surface structures were fabricated lithographically on the sample chamber cover slip from SU 8 photoresist.We present simultaneous stretching and TIRF imaging of double stranded DNA from the bacteriophage lambda. The DNA is stained with SyBR Gold (Invitrogen) and is bound to optically trapped dielectric beads in a dumbbell configuration. This technology will be applied to follow polymerase reactions in real time.[1] Lang, M.J. et al. (2004) Nature Methods. 1(2) 1 7.[2] Moerner, W.E. and Fromm, D.P. (2003) Review of Scientific instruments. 74(8) 3597 3619.[3] Harada Y. et al. (1999) Biophysical Journal. 76(2) 709 715.[4] Wallin, A.E. et al. (2008) Applied Physics Letters 92 224104.
author_names: Kalle Hanhijarvi

Heikki Ojala

Anders E Wallin

Gabija Ziedaite

Susanna Aura

Sami Franssila

Dennis H Bamford

Edward Haeggstrom
title: Simultaneous TIRF Microscopy and Optical Trapping for Single Molecule Experiments
year: 2011