Multispecies effects in the equilibrium and out-of-equilibrium thermostatistics of overdamped motion

Progress has been recently made, both theoretical and experimental, regarding the thermostatistics of complex systems of interacting particles or agents (species) obeying a nonlinear Fokker-Planck dynamics. However, major advances along these lines have been restricted to systems consisting of only one type of species. The aim of the present contribution is to overcome that limitation, going beyond single-species scenarios. We investigate the dynamics of overdamped motion in interacting and confined many-body systems having two or more species that experience different intra- A nd interspecific forces in a regime where forces arising from standard thermal noise can be neglected. Even though these forces are neglected, the behavior of the system can be analyzed in terms of an appropriate thermostatistical formalism. By recourse to a mean-field treatment, we derive a set of coupled nonlinear Fokker-Planck equations governing the behavior of these systems. We obtain an H theorem for this Fokker-Planck dynamics and discuss in detail an example admitting an exact, analytical stationary solution.Fil: Plastino, Ángel Ricardo. Universidad Nacional del Noroeste de la Provincia de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nobre, F. D.. Centro Brasileiro de Pesquisas Físicas; BrasilFil: Wedemann, R. S.. Universidade do Estado de Rio do Janeiro; Brasi

Nonlinear drag forces and the thermostatistics of overdamped motion

Diverse processes in statistical physics are usually analyzed on the assumption that the drag force acting on a test particle moving in a resisting medium is linear on the velocity of the particle. However, nonlinear drag forces do appear in relevant situations that are currently the focus of experimental and theoretical work. Motivated by these developments, we explore the consequences of nonlinear drag forces for the thermostatistics of systems of interacting particles performing overdamped motion. We derive a family of nonlinear Fokker-Planck equations for these systems, taking into account the effects of nonlinear drag forces. We investigate the main properties of these evolution equations, including an H-theorem, and obtain exact solutions of the stretched q-exponential form.Fil: Plastino, Ángel Ricardo. Universidad Nacional del Noroeste de la Provincia de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Wedemann, R. S.. Universidade do Estado de Rio do Janeiro; BrasilFil: Curado, E. M. F.. Centro Brasileiro de Pesquisas Físicas; BrasilFil: Nobre, F. D.. Centro Brasileiro de Pesquisas Físicas; BrasilFil: Tsallis, C.. Centro Brasileiro de Pesquisas Físicas; Brasi

Parallel high-performance grid computing: Capabilities and opportunities of a novel demanding service and business class allowing highest resource efficiency

Especially in the life-science and the health-care sectors the huge IT requirements are imminent due to the large and complex systems to be analysed and simulated. Grid infrastructures play here a rapidly increasing role for research, diagnostics, and treatment, since they provide the necessary large-scale resources efficiently. Whereas grids were first used for huge number crunching of trivially parallelizable problems, increasingly parallel high-performance computing is required. Here, we show for the prime example of molecular dynamic simulations how the presence of large grid clusters including very fast network interconnects within grid infrastructures allows now parallel high-performance grid computing efficiently and thus combines the benefits of dedicated super-computing centres and grid infrastructures. The demands for this service class are the highest since the user group has very heterogeneous requirements: i) two to many thousands of CPUs, ii) different memory architectures, iii) huge storage capabilities, and iv) fast communication via network interconnects, are all needed in different combinations and must be considered in a highly dedicated manner to reach highest performance efficiency. Beyond, advanced and dedicated i) interaction with users, ii) the management of jobs, iii) accounting, and iv) billing, not only combines classic with parallel high-performance grid usage, but more importantly is also able to increase the efficiency of IT resource providers. Consequently, the mere "yes-we- can" becomes a huge opportunity like e.g. the life-science and health-care sectors as well as grid infrastructures by reaching higher level of resource efficiency

Are Metastases from Metastases Clinical Relevant? Computer Modelling of Cancer Spread in a Case of Hepatocellular Carcinoma

Background: Metastasis formation remains an enigmatic process and one of the main questions recently asked is whether metastases are able to generate further metastases. Different models have been proposed to answer this question; however, their clinical significance remains unclear. Therefore a computer model was developed that permits comparison of the different models quantitatively with clinical data and that additionally predicts the outcome of treatment interventions. Methods: The computer model is based on discrete events simulation approach. On the basis of a case from an untreated patient with hepatocellular carcinoma and its multiple metastases in the liver, it was evaluated whether metastases are able to metastasise and in particular if late disseminated tumour cells are still capable to form metastases. Additionally, the resection of the primary tumour was simulated. The simulation results were compared with clinical data. Results: The simulation results reveal that the number of metastases varies significantly between scenarios where metastases metastasise and scenarios where they do not. In contrast, the total tumour mass is nearly unaffected by the two different modes of metastasis formation. Furthermore, the results provide evidence that metastasis formation is an early event and that late disseminated tumour cells are still capable of forming metastases. Simulations also allow estimating how the resection of the primary tumour delays the patient’s death. Conclusion: The simulation results indicate that for this particular case of a hepatocellular carcinoma late metastases, i.e.

Chromatin and epigenetics: current biophysical views

Recent advances in high-throughput sequencing experiments and their theoretical descriptions have determined fast dynamics of the "chromatin and epigenetics" field, with new concepts appearing at high rate. This field includes but is not limited to the study of DNA-protein-RNA interactions, chromatin packing properties at different scales, regulation of gene expression and protein trafficking in the cell nucleus, binding site search in the crowded chromatin environment and modulation of physical interactions by covalent chemical modifications of the binding partners. The current special issue does not pretend for the full coverage of the field, but it rather aims to capture its development and provide a snapshot of the most recent concepts and approaches. Eighteen open-access articles comprising this issue provide a delicate balance between current theoretical and experimental biophysical approaches to uncover chromatin structure and understand epigenetic regulation, allowing free flow of new ideas and preliminary results