TopicNeuro

biophysics

14 Seminars1 Position1 ePoster

Latest

PositionNeuroscience

N/A

Center for Neuroscience and Cell Biology of the University of Coimbra (CNC-UC)
Coimbra and Cantanhede, University of Coimbra
Jan 4, 2026

The PostDoctoral researcher will conduct research activities in modelling and simulation of reward-modulated prosocial behavior and decision-making. The position is part of a larger effort to uncover the computational and mechanistic bases of prosociality and empathy at the behavioral and circuit levels. The role involves working at the interface between experimental data (animal behavior and electrophysiology) and theoretical modelling, with an emphasis on Multi-Agent Reinforcement Learning and neural population dynamics.

SeminarNeuroscience

“Brain theory, what is it or what should it be?”

Prof. Guenther Palm
University of Ulm
Jun 27, 2025

n the neurosciences the need for some 'overarching' theory is sometimes expressed, but it is not always obvious what is meant by this. One can perhaps agree that in modern science observation and experimentation is normally complemented by 'theory', i.e. the development of theoretical concepts that help guiding and evaluating experiments and measurements. A deeper discussion of 'brain theory' will require the clarification of some further distictions, in particular: theory vs. model and brain research (and its theory) vs. neuroscience. Other questions are: Does a theory require mathematics? Or even differential equations? Today it is often taken for granted that the whole universe including everything in it, for example humans, animals, and plants, can be adequately treated by physics and therefore theoretical physics is the overarching theory. Even if this is the case, it has turned out that in some particular parts of physics (the historical example is thermodynamics) it may be useful to simplify the theory by introducing additional theoretical concepts that can in principle be 'reduced' to more complex descriptions on the 'microscopic' level of basic physical particals and forces. In this sense, brain theory may be regarded as part of theoretical neuroscience, which is inside biophysics and therefore inside physics, or theoretical physics. Still, in neuroscience and brain research, additional concepts are typically used to describe results and help guiding experimentation that are 'outside' physics, beginning with neurons and synapses, names of brain parts and areas, up to concepts like 'learning', 'motivation', 'attention'. Certainly, we do not yet have one theory that includes all these concepts. So 'brain theory' is still in a 'pre-newtonian' state. However, it may still be useful to understand in general the relations between a larger theory and its 'parts', or between microscopic and macroscopic theories, or between theories at different 'levels' of description. This is what I plan to do.

SeminarNeuroscienceRecording

How fly neurons compute the direction of visual motion

Axel Borst
Max-Planck-Institute for Biological Intelligence
Oct 9, 2023

Detecting the direction of image motion is important for visual navigation, predator avoidance and prey capture, and thus essential for the survival of all animals that have eyes. However, the direction of motion is not explicitly represented at the level of the photoreceptors: it rather needs to be computed by subsequent neural circuits, involving a comparison of the signals from neighboring photoreceptors over time. The exact nature of this process represents a classic example of neural computation and has been a longstanding question in the field. Much progress has been made in recent years in the fruit fly Drosophila melanogaster by genetically targeting individual neuron types to block, activate or record from them. Our results obtained this way demonstrate that the local direction of motion is computed in two parallel ON and OFF pathways. Within each pathway, a retinotopic array of four direction-selective T4 (ON) and T5 (OFF) cells represents the four Cartesian components of local motion vectors (leftward, rightward, upward, downward). Since none of the presynaptic neurons is directionally selective, direction selectivity first emerges within T4 and T5 cells. Our present research focuses on the cellular and biophysical mechanisms by which the direction of image motion is computed in these neurons.

SeminarNeuroscience

Setting network states via the dynamics of action potential generation

Susanne Schreiber
Humboldt University Berlin, Germany
Oct 5, 2022

To understand neural computation and the dynamics in the brain, we usually focus on the connectivity among neurons. In contrast, the properties of single neurons are often thought to be negligible, at least as far as the activity of networks is concerned. In this talk, I will contradict this notion and demonstrate how the biophysics of action-potential generation can have a decisive impact on network behaviour. Our recent theoretical work shows that, among regularly firing neurons, the somewhat unattended homoclinic type (characterized by a spike onset via a saddle homoclinic orbit bifurcation) particularly stands out: First, spikes of this type foster specific network states - synchronization in inhibitory and splayed-out/frustrated states in excitatory networks. Second, homoclinic spikes can easily be induced by changes in a variety of physiological parameters (like temperature, extracellular potassium, or dendritic morphology). As a consequence, such parameter changes can even induce switches in network states, solely based on a modification of cellular voltage dynamics. I will provide first experimental evidence and discuss functional consequences of homoclinic spikes for the design of efficient pattern-generating motor circuits in insects as well as for mammalian pathologies like febrile seizures. Our analysis predicts an interesting role for homoclinic action potentials as an integral part of brain dynamics in both health and disease.

SeminarNeuroscienceRecording

The Standard Model of the Retina

Markus Meister
Caltech
May 25, 2022

The science of the retina has reached an interesting stage of completion. There exists now a consensus standard model of this neural system - at least in the minds of many researchers - that serves as a baseline against which to evaluate new claims. The standard model links phenomena from molecular biophysics, cell biology, neuroanatomy, synaptic physiology, circuit function, and visual psychophysics. It is further supported by a normative theory explaining what the purpose is of processing visual information this way. Most new reports of retinal phenomena fit squarely within the standard model, and major revisions seem increasingly unlikely. Given that our understanding of other brain circuits with comparable complexity is much more rudimentary, it is worth considering an example of what success looks like. In this talk I will summarize what I think are the ingredients that led to this mature understanding of the retina. Equally important, a number of practices and concepts that are currently en vogue in neuroscience were not needed or indeed counterproductive. I look forward to debating how these lessons might extend to other areas of brain research.

SeminarNeuroscience

Homeostatic Plasticity in Health and Disease

Graeme Davis
UCSF, Department of Biochemistry and Biophysics Director, Kavli Institute for Fundamental Neuroscience
Apr 4, 2022

Dr. Davis will present a summary regarding the identification and characterization of mechanisms of homeostatic plasticity as they relate to the control of synaptic transmission. He will then provide evidence of translation to the mammalian neuromuscular junction and central synapses, and provide tangible links to the etiology of neurological disease.

SeminarNeuroscienceRecording

Retinoblastoma: Canadian global leadership

Brenda Gallie
Hospital for Sick Children, Alberta Children’s Hospital, Techna Institute and Krembil Research Institute, University Health Network, Departments Ophthalmology, Medical Biophysics, Molecular Genetics, University of Toronto.
Nov 16, 2021
SeminarNeuroscienceRecording

Analyzing Retinal Disease Using Electron Microscopic Connectomics

John Dowling
Harvard University
Sep 15, 2021

John DowlingJohn E. Dowling received his AB and PhD from Harvard University. He taught in the Biology Department at Harvard from 1961 to 1964, first as an Instructor, then as assistant professor. In 1964 he moved to Johns Hopkins University, where he held an appointment as associate professor of Ophthalmology and Biophysics. He returned to Harvard as professor of Biology in 1971, was the Maria Moors Cabot Professor of Natural Sciences from 1971-2001, Harvard College professor from 1999-2004 and is presently the Gordon and Llura Gund Professor of Neurosciences. Dowling was chairman of the Biology Department at Harvard from 1975 to 1978 and served as associate dean of the faculty of Arts and Sciences from 1980 to 1984. He was Master of Leverett House at Harvard from 1981-1998 and currently serves as president of the Corporation of The Marine Biological Laboratory in Woods Hole. He is a Fellow of the American Academy of Arts and Sciences, a member of the National Academy of Sciences and a member of the American Philosophical Society. Awards that Dowling received include the Friedenwald Medal from the Association of Research in Ophthalmology and Vision in 1970, the Annual Award of the New England Ophthalmological Society in 1979, the Retinal Research Foundation Award for Retinal Research in 1981, an Alcon Vision Research Recognition Award in 1986, a National Eye Institute's MERIT award in 1987, the Von Sallman Prize in 1992, The Helen Keller Prize for Vision Research in 2000 and the Llura Ligget Gund Award for Lifetime Achievement and Recognition of Contribution to the Foundation Fighting Blindness in 2001. He was granted an honorary MD degree by the University of Lund (Sweden) in 1982 and an honorary Doctor of Laws degree from Dalhousie University (Canada) in 2012. Dowling's research interests have focused on the vertebrate retina as a model piece of the brain. He and his collaborators have long been interested in the functional organization of the retina, studying its synaptic organization, the electrical responses of the retinal neurons, and the mechanisms underlying neurotransmission and neuromodulation in the retina. Dowling became interested in zebrafish as a system in which one could explore the development and genetics of the vertebrate retina about 20 years ago. Part of his research team has focused on retinal development in zebrafish and the role of retinoic acid in early eye and photoreceptor development. A second group has developed behavioral tests to isolate mutations, both recessive and dominant, specific to the visual system.

SeminarNeuroscienceRecording

Interpreting the Mechanisms and Meaning of Sensorimotor Beta Rhythms with the Human Neocortical Neurosolver (HNN) Neural Modeling Software

Stephanie Jones
Brown University
Sep 8, 2021

Electro- and magneto-encephalography (EEG/MEG) are the leading methods to non-invasively record human neural dynamics with millisecond temporal resolution. However, it can be extremely difficult to infer the underlying cellular and circuit level origins of these macro-scale signals without simultaneous invasive recordings. This limits the translation of E/MEG into novel principles of information processing, or into new treatment modalities for neural pathologies. To address this need, we developed the Human Neocortical Neurosolver (HNN: https://hnn.brown/edu ), a new user-friendly neural modeling tool designed to help researchers and clinicians interpret human imaging data. A unique feature of HNN’s model is that it accounts for the biophysics generating the primary electric currents underlying such data, so simulation results are directly comparable to source localized data. HNN is being constructed with workflows of use to study some of the most commonly measured E/MEG signals including event related potentials, and low frequency brain rhythms. In this talk, I will give an overview of this new tool and describe an application to study the origin and meaning of 15-29Hz beta frequency oscillations, known to be important for sensory and motor function. Our data showed that in primary somatosensory cortex these oscillations emerge as transient high power ‘events’. Functionally relevant differences in averaged power reflected a difference in the number of high-power beta events per trial (“rate”), as opposed to changes in event amplitude or duration. These findings were consistent across detection and attention tasks in human MEG, and in local field potentials from mice performing a detection task. HNN modeling led to a new theory on the circuit origin of such beta events and suggested beta causally impacts perception through layer specific recruitment of cortical inhibition, with support from invasive recordings in animal models and high-resolution MEG in humans. In total, HNN provides an unpresented biophysically principled tool to link mechanism to meaning of human E/MEG signals.

SeminarNeuroscienceRecording

Novel Object Detection and Multiplexed Motion Representation in Retinal Bipolar Cells

Alon Poleg-Polsky
Department of Physiology and Biophysics, University of Colorado School of Medicine
Jul 7, 2021

Detection of motion is essential for survival, but how the visual system processes moving stimuli is not fully understood. Here, based on a detailed analysis of glutamate release from bipolar cells, we outline the rules that govern the representation of object motion in the early processing stages. Our main findings are as follows: (1) Motion processing begins already at the first retinal synapse. (2) The shape and the amplitude of motion responses cannot be reliably predicted from bipolar cell responses to stationary objects. (3) Enhanced representation of novel objects - particularly in bipolar cells with transient dynamics. (4) Response amplitude in bipolar cells matches visual salience reported in humans: suddenly appearing objects > novel motion > existing motion. These findings can be explained by antagonistic interactions in the center-surround receptive field, demonstrate that despite their simple operational concepts, classical center-surround receptive fields enable sophisticated visual computations.

SeminarNeuroscience

K+ Channel Gain of Function in Epilepsy, from Currents to Networks

Matthew Weston
University of Vermont
Oct 21, 2020

Recent human gene discovery efforts show that gain-of-function (GOF) variants in the KCNT1gene, which encodes a Na+-activated K+ channel subunit, cause severe epilepsies and other neurodevelopmental disorders. Although the impact of these variants on the biophysical properties of the channels is well characterized, the mechanisms that link channel dysfunction to cellular and network hyperexcitability and human disease are unknown. Furthermore, precision therapies that correct channel biophysics in non-neuronal cells have had limited success in treating human disease, highlighting the need for a deeper understanding of how these variants affect neurons and networks. To address this gap, we developed a new mouse model with a pathogenic human variant knocked into the mouse Kcnt1gene. I will discuss our findings on the in vivo phenotypes of this mouse, focusing on our characterization of epileptiform neural activity using electrophysiology and widefield Ca++imaging. I will also talk about our investigations at the synaptic, cellular, and circuit levels, including the main finding that cortical inhibitory neurons in this model show a reduction in intrinsic excitability and action potential generation. Finally, I will discuss future directions to better understand the mechanisms underlying the cell-type specific effects, as well as the link between the cellular and network level effects of KCNT1 GOF.

SeminarNeuroscience

Towards multipurpose biophysics-based mathematical models of cortical circuits

Gaute Einevoll
Norwegian University of Life Sciences
Oct 14, 2020

Starting with the work of Hodgkin and Huxley in the 1950s, we now have a fairly good understanding of how the spiking activity of neurons can be modelled mathematically. For cortical circuits the understanding is much more limited. Most network studies have considered stylized models with a single or a handful of neuronal populations consisting of identical neurons with statistically identical connection properties. However, real cortical networks have heterogeneous neural populations and much more structured synaptic connections. Unlike typical simplified cortical network models, real networks are also “multipurpose” in that they perform multiple functions. Historically the lack of computational resources has hampered the mathematical exploration of cortical networks. With the advent of modern supercomputers, however, simulations of networks comprising hundreds of thousands biologically detailed neurons are becoming feasible (Einevoll et al, Neuron, 2019). Further, a large-scale biologically network model of the mouse primary visual cortex comprising 230.000 neurons has recently been developed at the Allen Institute for Brain Science (Billeh et al, Neuron, 2020). Using this model as a starting point, I will discuss how we can move towards multipurpose models that incorporate the true biological complexity of cortical circuits and faithfully reproduce multiple experimental observables such as spiking activity, local field potentials or two-photon calcium imaging signals. Further, I will discuss how such validated comprehensive network models can be used to gain insights into the functioning of cortical circuits.

SeminarNeuroscienceRecording

CRISPR-based functional genomics in iPSC-based models of brain disease

Martin Kampmann
UCSF Department of Biochemistry and Biophysics
Jul 30, 2020

Human genes associated with brain-related diseases are being discovered at an accelerating pace. A major challenge is an identification of the mechanisms through which these genes act, and of potential therapeutic strategies. To elucidate such mechanisms in human cells, we established a CRISPR-based platform for genetic screening in human iPSC-derived neurons, astrocytes and microglia. Our approach relies on CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa), in which a catalytically dead version of the bacterial Cas9 protein recruits transcriptional repressors or activators, respectively, to endogenous genes to control their expression, as directed by a small guide RNA (sgRNA). Complex libraries of sgRNAs enable us to conduct genome-wide or focused loss-of-function and gain-of-function screens. Such screens uncover molecular players for phenotypes based on survival, stress resistance, fluorescent phenotypes, high-content imaging and single-cell RNA-Seq. To uncover disease mechanisms and therapeutic targets, we are conducting genetic modifier screens for disease-relevant cellular phenotypes in patient-derived neurons and glia with familial mutations and isogenic controls. In a genome-wide screen, we have uncovered genes that modulate the formation of disease-associated aggregates of tau in neurons with a tauopathy-linked mutation (MAPT V337M). CRISPRi/a can also be used to model and functionally evaluate disease-associated changes in gene expression, such as those caused by eQTLs, haploinsufficiency, or disease states of brain cells. We will discuss an application to Alzheimer’s Disease-associated genes in microglia.

ePosterNeuroscience

Bridging biophysics and computation with differentiable simulation

Michael Deistler, Kyra Kadhim, Jonas Beck, Matthijs Pals, Janne Lappalainen, Manuel Gloeckler, Ziwei Huang, Cornelius Schroeder, Philipp Berens, Pedro Gonçalves, Jakob Macke

Bernstein Conference 2024

biophysics coverage

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