Non-standard discretization of biological models

We consider certain types of discretization schemes for differential equations with quadratic nonlinearities, which were introduced by Kahan, and considered in a broader setting by Mickens. These methods have the property that they preserve important structural features of the original systems, such as the behaviour of solutions near to fixed points, and also, where appropriate (e.g. for certain mechanical systems), the property of being volume-preserving, or preserving a symplectic/Poisson structure. Here we focus on the application of Kahan's method to models of biological systems, in particular to reaction kinetics governed by the Law of Mass Action, and present a general approach to birational discretization, which is applied to population dynamics of Lotka-Volterra type

Investigating Biological Matter with Theoretical Nuclear Physics Methods

The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such systems, collective excitations, cooperative transitions and phase transitions emerge as the result of the interplay of strong correlations with quantum or thermal fluctuations. In view of such an observation, some theoretical methods initially developed in the context of theoretical nuclear physics have been adapted to investigate the dynamics of biomolecules. In this talk, we review some of our recent studies performed along this direction. In particular, we discuss how the path integral formulation of the molecular dynamics allows to overcome some of the long-standing problems and limitations which emerge when simulating the protein folding dynamics at the atomistic level of detail.Comment: Prepared for the proceedings of the "XII Meeting on the Problems of Theoretical Nuclear Physics" (Cortona11

A Regularized Boundary Element Formulation for Contactless SAR Evaluations within Homogeneous and Inhomogeneous Head Phantoms

This work presents a Boundary Element Method (BEM) formulation for contactless electromagnetic field assessments. The new scheme is based on a regularized BEM approach that requires the use of electric measurements only. The regularization is obtained by leveraging on an extension of Calderon techniques to rectangular systems leading to well-conditioned problems independent of the discretization density. This enables the use of highly discretized Huygens surfaces that can be consequently placed very near to the radiating source. In addition, the new regularized scheme is hybridized with both surfacic homogeneous and volumetric inhomogeneous forward BEM solvers accelerated with fast matrix-vector multiplication schemes. This allows for rapid and effective dosimetric assessments and permits the use of inhomogeneous and realistic head phantoms. Numerical results corroborate the theory and confirms the practical effectiveness of all newly proposed formulations

Thermodynamics and Phase Transitions of Electrolytes on Lattices with Different Discretization Parameters

Lattice models are crucial for studying thermodynamic properties in many physical, biological and chemical systems. We investigate Lattice Restricted Primitive Model (LRPM) of electrolytes with different discretization parameters in order to understand thermodynamics and the nature of phase transitions in the systems with charged particles. A discretization parameter is defined as a number of lattice sites that can be occupied by each particle, and it allows to study the transition from the discrete picture to the continuum-space description. Explicit analytic and numerical calculations are performed using lattice Debye-H\"{u}ckel approach, which takes into account the formation of dipoles, the dipole-ion interactions and correct lattice Coulomb potentials. The gas-liquid phase separation is found at low densities of charged particles for different types of lattices. The increase in the discretization parameter lowers the critical temperature and the critical density, in agreement with Monte Carlo computer simulations results. In the limit of infinitely large discretization our results approach the predictions from the continuum model of electrolytes. However, for the very fine discretization, where each particle can only occupy one lattice site, the gas-liquid phase transitions are suppressed by order-disorder phase transformations.Comment: Submitted to Molecular Physic

First-order phase transition of the tethered membrane model on spherical surfaces

We found that three types of tethered surface model undergo a first-order phase transition between the smooth and the crumpled phase. The first and the third are discrete models of Helfrich, Polyakov, and Kleinert, and the second is that of Nambu and Goto. These are curvature models for biological membranes including artificial vesicles. The results obtained in this paper indicate that the first-order phase transition is universal in the sense that the order of the transition is independent of discretization of the Hamiltonian for the tethered surface model.Comment: 22 pages with 14 figure