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Mechanically induced crystallographic phase transformation that reflects dynamic stress responses of intrinsically stochastic nature is a pertinent yet much less well-understood phenomenon. We focus on understanding the physical…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…
From the analysis of the measurement process we make the hypothesis that we have to add to the quantum state psi a label z and a special function alpha in order to describe completely the preparation of a (pure) quantum system . Given such…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
The dynamics of phase transitions plays a crucial r\^ole in the so-called interface between high energy particle physics and cosmology. Many of the interesting results generated during the last fifteen years or so rely on simplified…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
The connection between the thermodynamics of charged finite nuclear systems and the asymptotically measured partitions is presented. Some open questions, concerning in particular equilibrium partitions are discussed. We show a detailed…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
One of the most striking many-body phenomena in nature is the sudden change of macroscopic properties as the temperature or energy reaches a critical value. Such equilibrium transitions have been predicted and observed in two and three…
We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a…
Random walks on multidimensional nonlinear landscapes are of interest in many areas of science and engineering. In particular, properties of adaptive trajectories on fitness landscapes determine population fates and thus play a central role…
Major efforts in recent years have been directed towards understanding molecular transport in polymeric membranes, in particular reverse osmosis and nanofiltration membranes. Transition-state theory is an increasingly common approach to…