Related papers: A Statistical Mechanical Approach to Protein Aggre…
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic…
The Hamiltonian of an isolated quantum mechanical system determines its dynamics and physical behaviour. This study investigates the possibility of learning and utilising a system's Hamiltonian and its variational thermal state estimation…
Efficient bacterial chromosome segregation typically requires the coordinated action of a three-components, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the…
Colloidal systems offer unique opportunities for the study of phase formation and structure since their characteristic length scales are accessible to visible light. As a model system the two dimensional assembly of colloidal magnetic and…
Widely used closed product-form networks have emerged recently as a primary model of stochastic growth of sub-cellular structures, e.g., cellular filaments. In the baseline model, homogeneous monomers attach and detach stochastically to…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical…
Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein…
We develop the partitioning technique for quantum discrete systems. The graph consists of several subgraphs: a central graph and several branch graphs, with each branch graph being rooted by an individual node on the central one. We show…
Statistical mechanics and thermodynamics for ideal fractional exclusion statistics with mutual statistical interactions is studied systematically. We discuss properties of the single-state partition functions and derive the general form of…
Mixture - modeling of mass spectra is an approach with many potential applications including peak detection and quantification, smoothing, de-noising, feature extraction and spectral signal compression. However, existing algorithms do not…
Under favourable conditions, many proteins can assemble into macroscopically large aggregate's, Parkinson's and other neurological and systemic diseases. The overall process of protein aggregation is characterized by initial lag time during…
We consider the physical combinatorics of critical lattice models and their associated conformal field theories arising in the continuum scaling limit. As examples, we consider A-type unitary minimal models and the level-1 sl(2)…
Many phenomena of strongly correlated materials are encapsulated in the Fermi-Hubbard model whose thermodynamical properties can be computed from its grand canonical potential according to standard procedures. In general, there is no closed…
Cellular aggregates play a significant role in the evolution of biological systems such as tumor growth, tissue spreading, wound healing, and biofilm formation. Analysis of such biological systems, in principle, includes examining the…
We show that a stochastic approach enables calculations of the optical properties of large 2-dimensional and nanotubular excitonic molecular aggregates. Previous studies of such systems relied on numerically diagonalizing the dense and…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
A simple statistical mechanical model proposed by Wako and Sait$\hat{\rm o}$ has explained the aspects of protein folding surprisingly well. This model was systematically applied to multiple proteins by Mu$\tilde{\rm n}$oz and Eaton and has…