Related papers: Multi-dimensional structure of C. elegans thermal …
Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an…
The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and…
Biological systems process information under noisy environment. Sensory adaptation model of E. coli is suitable for investigation because of its simplicity. To understand the adaptation processing quantitatively, stochastic thermodynamic…
Recent empirical studies found different thermodynamic phases for collective motion in animals. However, such a thermodynamic description for human movement remains unclear, mainly due to the limited resolution of existing tracking…
How do we capture the breadth of behavior in animal movement, from rapid body twitches to aging? Using high-resolution videos of the nematode worm $C. elegans$, we show that a single dynamics connects posture-scale fluctuations with…
The mechanical behaviors of polycrystalline solids are determined by the interplay between phenomena governed by two different thermodynamic temperatures: the configurational effective temperature that controls the density of dislocations,…
This thesis investigates the interactions of different degrees of freedom of one joint system within the theory of stochastic thermodynamics. First, a comprehensive introduction to the subjects of stochastic processes, information theory…
We investigate the heterogeneous dynamics in a model, where chemical gelation and glass transition interplay, focusing on the dynamical susceptibility. Two independent mechanisms give raise to the correlations, which are manifested in the…
An analytical method to compute thermodynamic properties of a given Hamiltonian system is proposed. This method combines ideas of both dynamical systems and ensemble approaches to thermodynamics, providing de facto a possible alternative to…
A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an implicit model of the environmental variables. The system's state retains information about past environmental fluctuations,…
A scenario for systems with slow dynamics is characterised by stating that there are several temperatures coexisting in the sample, with a single temperature shared by all observables at each (widely separate) time-scale. In preparation for…
Understanding principles of neurolocomotion requires the synthesis of neural activity, sensory feedback, and biomechanics. The nematode \textit{C. elegans} is an ideal model organism for studying locomotion in an integrated neuromechanical…
Neuromechanics aims to understand the link between an animal's neural activity and its physical behaviors. Recent advances in experimental and machine learning techniques enable simultaneous recordings of neural and locomotion dynamics over…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
We study theoretically and numerically a family of multi-point dynamic susceptibilities that quantify the strength and characteristic lengthscales of dynamic heterogeneities in glass-forming materials. We use general theoretical arguments…
We define a DNA as a sequence of $1, 2$'s and embed it on a path of Cayley tree in such a way that each vertex of the Cayley tree belongs only to one of DNA and each DNA has its own countably many set of neighboring DNAs. The Hamiltonian of…
In this study, we demonstrate the generalizability of graph neural networks in predicting the dynamic heterogeneity of model glass-forming liquids across different temperatures. While previous approaches have often been limited to making…
Data-driven modeling and control of temperature dynamics in mechatronics systems and industrial processes are challenging control engineering problems. This is mainly because the temperature dynamics is inherently infinite-dimensional,…
Aerotaxis is the particular form of chemotaxis in which oxygen plays the role of both the attractant and the repellent. Aerotaxis occurs without methylation adaptation, and it leads to fast and complete aggregation toward the most favorable…
The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…