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Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of…
We have developed a new simulation method to estimate the distance between the native state and the first transition state, and the distance between the intermediate state and the second transition state of a protein which mechanically…
Interpreting partial information collected from systems subject to noise is a key problem across scientific disciplines. Theoretical frameworks often focus on the dynamics of variables that result from coarse-graining the internal states of…
We use a simplified model which is based on the same physics as inherent in most statistical models for nuclear multifragmentation. The simplified model allows exact calculations for thermodynamic properties of systems of large number of…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
We study the scenarios of the dynamics of ternary statistical experiments, modeled employing difference equations. The important features are a balance condition and the existence of a steady-state (equilibrium). We give a classification of…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of…
Proteins evolve through complex sequence spaces, with fitness landscapes serving as a conceptual framework that links sequence to function. Fitness landscapes can be smooth, where multiple similarly accessible evolutionary paths are…
Modeling and simulating the protein folding process overall remains a grand challenge in computational biology. We systematically investigate end-to-end quantum algorithms for simulating various protein dynamics with effects, such as…
The topological theory of phase transitions was proposed on the basis of different arguments, the most important of which are: a direct evidence of the relation between topology and phase transitions for some exactly solvable models; an…
The nonequilibrium stationary state of an exclusive genetic switch is considered. The model comprises two competing species and a single binding site which, when bound to by a protein of one species, causes the other species to be…
We study an ideal-gas-like model where the particles exchange energy stochastically, through energy conserving scattering processes, which take place if and only if at least one of the two particles has energy below a certain energy…
The nature of the Abelian Higgs Model phase transition is investigated. A variational approximation is used in the evaluation of the relevant finite temperature effective potential. Some of the results presented are valid not only in the…
In order to better understand the occurrence of phase transitions, we adopt an approach based on the study of energy landscapes: The relation between stationary points of the potential energy landscape of a classical many-particle system…
Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central…
Inherent structure theory is used to discover strong connections between simple characteristics of protein structure and the energy landscape of a Go model. The potential energies and vibrational free energies of inherent structures are…
In this work a first attempt is made to extract the Equation of State (EoS) using experimental results of the $\phi$ meson produced in nuclear collisions at AGS, SPS and RHIC energies. The data are confronted to simple thermodynamic…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the…