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RNA polymerase (RNAP) is an enzyme that synthesizes a messenger RNA (mRNA) strand which is complementary to a single-stranded DNA template. From the perspective of physicists, an RNAP is a molecular motor that utilizes chemical energy input…

Biological Physics · Physics 2008-02-06 Tripti Tripathi , Debashish Chowdhury

Chromatin remodeling machineries are abundant and diverse in eukaryotic cells. They have been involved in a variety of situations such as histone exchange and DNA repair, but their importance in gene expression remains unclear. Although the…

Molecular Networks · Quantitative Biology 2015-09-25 Denis Michel

Using programmable analog quantum annealing processors, we implement a sampling-based magnetic hysteresis protocol to probe the counterintuitive notion of magnetic memory of antiferromagnets. A key component of this protocol responsible for…

Quantum Physics · Physics 2025-11-25 Elijah Pelofske , Pratik Sathe , Cristiano Nisoli , Frank Barrows

In this paper, we investigated the neural spikes synchronisation in a neural network with synaptic plasticity and external perturbation. In the simulations the neural dynamics is described by the Hodgkin Huxley model considering chemical…

Rhythmic activity has been associated with a wide range of cognitive processes. Previous studies have shown that spike-timing-dependent plasticity can facilitate the transfer of rhythmic activity downstream the information processing…

Neurons and Cognition · Quantitative Biology 2020-09-09 Nimrod Sherf , Maoz Shamir

Short-term synaptic depression and facilitation have been found to greatly influence the performance of autoassociative neural networks. However, only partial results, focused for instance on the computation of the maximum storage capacity…

Disordered Systems and Neural Networks · Physics 2015-06-03 J. F. Mejias , B. Hernandez-Gomez , J. J. Torres

The effect of the anisotropy in the exchange interaction and film thickness on the hysteresis behavior of the anisotropic Heisenberg thin film has been investigated with effective field formulation in a two spin cluster using the decoupling…

Statistical Mechanics · Physics 2016-08-24 Ümit Akıncı , Musa Atlıhan

Neural synchrony in the brain at rest is usually variable and intermittent, thus intervals of predominantly synchronized activity are interrupted by intervals of desynchronized activity. Prior studies suggested that this temporal structure…

Quantitative Methods · Quantitative Biology 2021-04-26 Joel Zirkle , Leonid L Rubchinsky

We report a detailed study of neuromorphic switching behaviour in inherently complex percolating networks of self-assembled metal nanoparticles. We show that variation of the strength and duration of the electric field applied to this…

Disordered Systems and Neural Networks · Physics 2019-03-06 S. K. Bose , S. Shirai , J. B. Mallinson , S. A. Brown

We show that the unavoidable increase in neuronal response latency to ongoing stimulation serves as a nonuniform gradual stretching of neuronal circuit delay loops and emerges as an essential mechanism in the formation of various types of…

Neurons and Cognition · Quantitative Biology 2012-12-07 Roni Vardi , Reut Timor , Shimon Marom , Moshe Abeles , Ido Kanter

We study the synchronization of two model neurons coupled through a synapse having an activity-dependent strength. Our synapse follows the rules of Spike-Timing Dependent Plasticity (STDP). We show that this plasticity of the coupling…

Biological Physics · Physics 2009-11-07 Valentin P. Zhigulin , Mikhail I. Rabinovich , Ramon Huerta , Henry D. I. Abarbanel

Non structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism…

Biomolecules · Quantitative Biology 2016-01-06 Andrea Pérez-Villa , Maria Darvas , Giovanni Bussi

In contrast to equilibrium systems, inertia can profoundly impact the phase behavior of active systems. This has been made particularly evident in recent years, with motility-induced phase separation (MIPS) exhibiting several intriguing…

Soft Condensed Matter · Physics 2025-04-21 Jiechao Feng , Ahmad K. Omar

Two-component Marangoni contracted droplets can be arranged into arbitrary two-dimensional tiling patterns where they display rich dynamics due to vapor mediated long-range interactions. Recent work has characterized the centered hexagonal…

Soft Condensed Matter · Physics 2023-10-05 Anton Molina , Manu Prakash

We investigate the synchronization properties between two excitatory coupled neurons in the presence of an inhibitory loop mediated by an interneuron. Dynamical inhibition together with noise independently applied to each neuron provide…

Neurons and Cognition · Quantitative Biology 2016-11-23 Fernanda S. Matias , Leonardo L. Gollo , Pedro V. Carelli , Claudio R. Mirasso , Mauro Copelli

We have added a simplified neuromorphic model of Spike Time Dependent Plasticity (STDP) to the Synapto-dendritic Kernel Adapting Neuron (SKAN). The resulting neuron model is the first to show synaptic encoding of afferent signal to noise…

Neural and Evolutionary Computing · Computer Science 2014-11-12 Saeed Afshar , Libin George , Jonathan Tapson , Andre van Schaik , Philip de Chazal , Tara Julia Hamilton

Experimental evidences show that in gene transcription, RNA polymerase has the possibility to be stalled at certain position of the transcription template. This may be due to the template damage, or protein barriers. Once stalled,…

Biological Physics · Physics 2015-02-10 Jingwei Li , Yunxin Zhang

The associative memory model is a typical neural network model, which can store discretely distributed fixed-point attractors as memory patterns. When the network stores the memory patterns extensively, however, the model has other…

Neurons and Cognition · Quantitative Biology 2014-11-27 Shin Murata , Yosuke Otsubo , Kenji Nagata , Masato Okada

Neuromodulation plays a fundamental role in the acquisition of new behaviours. Our experimental findings show that, whereas acetylcholine biases hippocampal synaptic plasticity towards depression, the subsequent application of dopamine can…

Neurons and Cognition · Quantitative Biology 2017-10-06 Sara Zannone , Zuzanna Brzosko , Ole Paulsen , Claudia Clopath

The cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable non-equilibrium processes ranging from mitosis to chemotaxis. Its versatile reconfigurability, programmed by interactions…

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