Determination of Interaction Potentials of Amino Acids from Native Protein Structures: Test on Simple Lattice Models

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also uncovers the shortcomings of any optimization procedure. The strategy can be applied on any data set of native structures such as those available from the Protein Data Bank (PDB). In this work, however, we explain and test our approach on simple lattice models, where the true interactions are known a priori. Excellent agreement is obtained between the extracted and the true potentials even for modest numbers of protein structures in the PDB. Comparisons with other methods are also discussed.Comment: 24 pages, 4 figure

Kinetic distance and kinetic maps from molecular dynamics simulation

Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly-interconverting states. Here we build upon diffusion map theory and define a kinetic distance for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine

Lower Bounds for Structuring Unreliable Radio Networks

In this paper, we study lower bounds for randomized solutions to the maximal independent set (MIS) and connected dominating set (CDS) problems in the dual graph model of radio networks---a generalization of the standard graph-based model that now includes unreliable links controlled by an adversary. We begin by proving that a natural geographic constraint on the network topology is required to solve these problems efficiently (i.e., in time polylogarthmic in the network size). We then prove the importance of the assumption that nodes are provided advance knowledge of their reliable neighbors (i.e, neighbors connected by reliable links). Combined, these results answer an open question by proving that the efficient MIS and CDS algorithms from [Censor-Hillel, PODC 2011] are optimal with respect to their dual graph model assumptions. They also provide insight into what properties of an unreliable network enable efficient local computation.Comment: An extended abstract of this work appears in the 2014 proceedings of the International Symposium on Distributed Computing (DISC

Smallpox vaccination-elicited antibodies cross-neutralize 2022-Monkeypox virus Clade II

Since early May 2022, some monkeypox virus (MPXV) infections have been reported from countries where the disease is not endemic. Within 2 months, the number of patients has increased extensively, becoming the most considerable MPXV outbreak described. Smallpox vaccines demonstrated high efficacy against MPXVs in the past and are considered a crucial outbreak control measure. However, viruses isolated during the current outbreak carry distinct genetic variations, and the cross-neutralizing capability of antibodies remains to be assessed. Here we report that serum antibodies elicited by first-generation smallpox vaccines can neutralize the current MPXV more than 40 years after vaccine administration

Relativistic coupled-cluster calculations of 20^{20}Ne, 40^{40}Ar, 84^{84}Kr and 129^{129}Xe: correlation energies and dipole polarizabilities

We have carried out a detailed and systematic study of the correlation energies of inert gas atoms Ne, Ar, Kr and Xe using relativistic many-body perturbation theory and relativistic coupled-cluster theory. In the relativistic coupled-cluster calculations, we implement perturbative triples and include these in the correlation energy calculations. We then calculate the dipole polarizability of the ground states using perturbed coupled-cluster theory.Comment: 10 figures, 6 tables, submitted to PR

POINT CLOUD EXPLOITATION FOR STRUCTURAL MODELING AND ANALYSIS: A RELIABLE WORKFLOW

none4noThe digitization and geometric knowledge of the historical built heritage is currently based on point cloud, that rarely or only partially is used as digital twin for structural analysis. The present work deals with historical artefacts survey, with particular reference to masonry structures, aimed to their structural analysis and assessment. In detail, the study proposes a methodology capable of employing semi-directly the original data obtained from the 3D digital survey for the generation of a Finite Element Model (FEM), used for structural analysis of masonry buildings. The methodology described presents a reliable workflow with twofold purpose: the improvement of the transformation process of the point cloud in solid and subsequently obtain a high-quality and detailed model for structural analyses. Through the application of the methodology to a case study, the method consistency was assessed, regarding the smoothness of the whole procedure and the dynamic characterization of the Finite Element Model. The main improvement in respect with similar or our previous workflows is obtained by the introduction of the retopology in data processing, allowing the transformation of the raw data into a solid model with optimal balancing between Level of Detail (LOD) and computational weight. Another significant aspect of the optimized process is undoubtedly the possibility of faithfully respecting the semantics of the structure, leading to the discretization of the model into different parts depending on the materials. This work may represent an excellent reference for the study of masonry artefacts belonging to the existing historical heritage, starting from surveys and with the purpose to structural and seismic evaluations, in the general framework of knowledge-based preservation of heritage.openLucidi, A.; Giordano, E.; Clementi, F.; Quattrini, R.Lucidi, A.; Giordano, E.; Clementi, F.; Quattrini, R

The Coulomb Interaction between Pion-Wavepackets: The piplus-piminus Puzzle

The time dependent Schr\"odinger equation for $\pi^+$--$\pi^-$ pairs, which are emitted from the interaction zone in relativistic nuclear collisions, is solved using wavepacket states. It is shown that the Coulomb enhancement in the momentum correlation function of such pairs is smaller than obtained in earlier calculations based on Coulomb distorted plane waves. These results suggest that the experimentally observed positive correlation signal cannot be caused by the Coulomb interaction between pions emitted from the interaction zone. But other processes which involve long-lived resonances and the related extended source dimensions could provide a possible explanation for the observed signal.Comment: 12 pages, LaTeX, 1 figur

Physical origin of the power-law tailed statistical distributions

Starting from the BBGKY hierarchy, describing the kinetics of nonlinear particle system, we obtain the relevant entropy and stationary distribution function. Subsequently, by employing the Lorentz transformations we propose the relativistic generalization of the exponential and logarithmic functions. The related particle distribution and entropy represents the relativistic extension of the classical Maxwell-Boltzmann distribution and of the Boltzmann entropy respectively and define the statistical mechanics presented in [Phys. Rev. E {\bf 66}, 056125 (2002)] and [Phys. Rev. E {\bf 72}, 036108 (2005). The achievements of the present effort, support the idea that the experimentally observed power law tailed statistical distributions in plasma physics, are enforced by the relativistic microscopic particle dynamics.Comment: 6 pages. arXiv admin note: substantial text overlap with arXiv:1110.3944, arXiv:1012.390

Factors influencing on Job decision of Management Undergraduates in North and East Universities of Sri Lanka

This paper attempts to investigate the preferences on taking the decision of Job and to find out the factors influencing on Job decision of the management undergraduate in North and East Universities of Sri Lanka. A closed ended questionnaire was developed as tool for data collection. A total number of 400 third and final year management students from 3 Universities and 2 Campuses located in North and East of Sri Lanka have been responded to the questionnaire. The quantitative analyses were conducted with the help of SPSS. The result reveals that majority of the respondents’ preferred for future career developments are public sector and private sector organizations. One third of the total respondents plan to seek employment in their chosen field specially after obtaining the bachelor's degree. Further Salary, interesting job, job security and educational opportunity are the major factors for the management graduates in Job decision. Keywords: Job decision, Management, Undergraduate, Universit

Capacity and delay scaling for broadcast transmission in highly mobile wireless networks

We study broadcast capacity and minimum delay scaling laws for highly mobile wireless networks, in which each node has to disseminate or broadcast packets to all other nodes in the network. In particular, we consider a cell partitioned network under the simplifed independent and identically distributed (IID) mobility model, in which each node chooses a new cell at random every time slot. We derive scaling laws for broadcast capacity and minimum delay as a function of the cell size. We propose a simple first-come-firstserve (FCFS) flooding scheme that nearly achieves both capacity and minimum delay scaling. Our results show that high mobility does not improve broadcast capacity, and that both capacity and delay improve with increasing cell sizes. In contrast to what has been speculated in the literature we show that there is (nearly) no tradeoff between capacity and delay. Our analysis makes use of the theory of Markov Evolving Graphs (MEGs) and develops two new bounds on ooding time in MEGs by relaxing the previously required expander property assumption. Keywords: Mobile ad hoc networks, Wireless networks, Broadcast, Throughputdelay tradeoff, Scaling laws, Flooding time, Markov evolving graphNational Science Foundation (U.S.) (Grant CNS-1217048)National Science Foundation (U.S.) (Grant CNS-1713725)National Science Foundation (U.S.) (Grant AST-1547331