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Globular clusters are collisional systems, meaning that the stars inside them interact on timescales much shorter than the age of the Universe. These frequent interactions transfer energy between stars and set up observable trends that tell…
Critical phase transitions have proven to be a powerful concept to capture the phenomenology of many systems, including deeply non-equilibrium ones like living systems. The study of these phase transitions has overwhelmingly relied on…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
Face-to-face interactions reveal recurring patterns, suggesting the possibility of shared underlying mechanisms. More specifically, inter-contact durations, contact durations and number of contacts per edge share similar heavy-tail…
The sticking of a soft polystyrene colloidal particle to a planar glass plate was studied by a microrheological technique using an optical tweezer to trap the particle and a piezoelectric-stage to position the plate and to sinusoidally…
We have studied the kinetics of cluster formation for dynamical systems of dimensions up to $n=8$ interacting through elastic collisions or coalescence. These systems could serve as possible models for gas kinetics, polymerization and…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
We consider the stochastic patterns of a system of communicating, or coupled, self-propelled particles in the presence of noise and communication time delay. For sufficiently large environmental noise, there exists a transition between a…
Nucleation during solidification in multi-component alloys is a complex process that comprises the competition between different crystalline phases as well as chemical composition and ordering. Here, we combine transition interface sampling…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to…
Given a set of variables and the correlations among them, we develop a method for finding clustering among the variables. The method takes advantage of information implicit in higher-order (not just pairwise) correlations. The idea is to…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
S-adenosylhomocysteine hydrolase (SAHH), a cellular enzyme that plays a key role in methylation reactions including those required for maturation of viral mRNA, is an important drug target in the discovery of antiviral agents. While…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…