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The linear noise approximation models the random fluctuations from the mean-field model of a chemical reaction that unfolds near the thermodynamic limit. Specifically, the fluctuations obey a linear Langevin equation up to order…
Biological systems produce outputs in response to variable inputs. Input-output relations tend to follow a few regular patterns. For example, many chemical processes follow the S-shaped Hill equation relation between input concentrations…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…
We report a molecular dynamics (MD) study of the collective dynamics of a simple monatomic liquid -interacting through a two body potential that mimics that of lithium- across the liquid-glass transition. In the glassy phase we find…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated…
The movement of single kinesin molecules was observed while applying noisy external forces that mimic intracellular active fluctuations. We found kinesin accelerates under noise, especially when a large hindering load is added. The behavior…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
The paper gives a systematic analysis of singularities of transition processes in dynamical systems. General dynamical systems with dependence on parameter are studied. A system of relaxation times is constructed. Each relaxation time…
The concept of limiting step gives the limit simplification: the whole network behaves as a single step. However, in its simplest form this idea is applicable only to the simplest linear cycles in steady states. For such the simplest cycles…
We explore the limitations and validity of semi-classically formulated spin equations of motion. Using a single-molecule magnet as a test model, we employ three qualitatively different approximation schemes. From a microscopic model, we…
The efficient calculation of rare-event kinetics in complex dynamical systems, such as the rate and pathways of ligand dissociation from a protein, is a generally unsolved problem. Markov state models can systematically integrate ensembles…
The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems…
Conventional analysis of in vitro assays of motor proteins rests on the assumption that all proteins with the same chemical composition function identically; however molecule-to-molecule variation is often seen even in well-controlled…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…
Complementary Neutron Spin Echo and X-ray experiments and Molecular Dynamics simulations have been performed on difluorotetrachloroethane (CFCl2-CFCl2) glassy crystal. Static, single-molecule reorientational dynamics and collective dynamics…
Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities…
Virtually every biological function emerges through the organization of molecules in time and space. Consequently, a major challenge in statistical physics is to uncover the universal principles governing macromolecular self-organization…
Stochastic modeling of transcription is a classic yet long-standing problem in theoretical biophysics. The lack of unified results and a computationally efficient approach for a general, fine-grained transcription model has confined…
Using molecular dynamics simulations we investigate the finite-size dependence of the dynamical properties of a diatomic supercooled liquid. The simplicity of the molecule permits us to access the microsecond time scale. We find that the…