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The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular…
The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
We consider possible designs and experimental realiza-tions in synthesized rather than naturally occurring bio-chemical systems of a selection of basic bio-inspired information processing steps. These include feed-forward loops, which have…
We discuss a curious example for the collective mechanical behavior of coupled non-linear monomer units entrapped in a circular filament. Within a simple model we elucidate how multistability of monomer units and exponentially large…
Balancing influential covariates is crucial for valid treatment comparisons in clinical studies. While covariate-adaptive randomization is commonly used to achieve balance, its performance can be inadequate when the number of baseline…
Accurate prediction of protein-ligand binding poses is crucial for structure-based drug design, yet existing methods struggle to balance speed, accuracy, and physical plausibility. We introduce Matcha, a novel molecular docking pipeline…
Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed…
Genetic inactivation of essential genes creates an evolutionary scenario distinct from escape from drug inhibition, but the mechanisms of microbe adaptations in such cases remain unknown. Here we inactivate E. coli dihydrofolate reductase…
For cellular functions like division and polarization, protein pattern formation driven by NTPase cycles is a central spatial control strategy. Operating far from equilibrium, no general theory links microscopic reaction networks and…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Many different processes take place to facilitate lubrication of the joints functioning in human locomotion system. The main purpose of this is to avoid destroying the articular cartilage. Viscoelastic properties of the joints system are…
e discuss the relevance of the Stillinger and Weber approach to the glass transition investigating the non-equilibrium behavior of models with non-trivial dynamics, but with simple equilibrium properties. We consider a family of 1D…
Here, we discuss a collection of cutting-edge techniques and applications in use today by some of the leading experts in the field of correlative approaches in single-molecule biophysics. A key difference in emphasis, compared with…