Related papers: Crowding induced entropy-enthalpy compensation in …
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
When birds come together to form a flock, the distribution of their individual velocities narrows around the mean velocity of the flock. We argue that, in a broad class of models for the joint distribution of positions and velocities, this…
A fundamental theory is presented for the mechanical response of polymer networks undergoing large deformation which seamlessly integrates statistical mechanical principles with macroscopic thermodynamic constitutive theory. Our formulation…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
Transport through nano-channels plays an important role in many biological processes and industrial applications. Gaining insights into the functioning of biological transport processes and the design of man-made nano-devices requires an…
We present analytic and numerical results for two models, namely the minority model and the bar-attendance model, which offer simple paradigms for a competitive marketplace. Both models feature heterogeneous agents with bounded rationality…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
Experimental studies of systems containing active proteins that undergo conformational changes driven by catalytic chemical reactions have shown that the diffusion coefficients of passive tracer particles and active molecules are larger…
Brownian dynamics simulations are an increasingly popular tool for understanding spatially-distributed biochemical reaction systems. Recent improvements in our understanding of the cellular environment show that volume exclusion effects are…
We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…
Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance,…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of…
Depletion forces and macromolecular crowding govern the structure and function of biopolymers in biological cells and the properties of polymer nanocomposite materials. To isolate and analyze the influence of polymer shape fluctuations and…
Random matrix theory successfully connects the structure of interactions of large ecological communities to their ability to respond to perturbations. One of the most debated aspects of this approach is the missing role of population…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
Effective interactions inherently encompass many-body effects that appear unified. Analyzing these in reverse, that is, separating them into contributions from pairs, triples, or larger groups, is typically intricate and seldom pursued.…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the…