Franciszek Rakowski

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Beth L. Chen6
David H. Hall6
Dmitri B. Chklovskii6
Seth A. Wescott5
M Chalfie5
7Harold A. Scheraga
7Adam Liwo
5Kristy J Lawton
5Serge Faumont
5Navin Pokala

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2003
2017

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Synaptic polarity of the interneuron circuit controlling C. elegans locomotion
Caenorhabditis elegans is the only animal for which a detailed neural connectivity diagram has been constructed. However, synaptic polarities in this diagram, and thus, circuit functions are largely unknown. Here, we deciphered the likely polarities of seven pre-motor neurons implicated in the control of worm's locomotion, using a combination of… (More)
Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode.
The Lagrange formalism was implemented to derive the equations of motion for the physics-based united-residue (UNRES) force field developed in our laboratory. The C(alpha)...C(alpha) and C(alpha)...SC (SC denoting a side-chain center) virtual-bond vectors were chosen as variables. The velocity Verlet algorithm was adopted to integrate the equations of… (More)
Large Scale Daily Contacts and Mobility Model - an Individual-Based Countrywide Simulation Study for Poland
In this study we describe a simulation platform used to create a virtual society of Poland, with a particular emphasis on contact patterns arising from daily commuting to schools or workplaces. In order to reproduce the map of contacts, we are using a geo-referenced Agent Based Model. Within this framework, we propose a set of different stochastic… (More)
Implementation of a symplectic multiple-time-step molecular dynamics algorithm, based on the united-residue mesoscopic potential energy function.
A symplectic multiple-time-step (MTS) algorithm has been developed for the united-residue (UNRES) force field. In this algorithm, the slow-varying forces (which contain most of the long-range interactions and are, therefore, expensive to compute) are integrated with a larger time step, termed the basic time step, and the fast-varying forces are integrated… (More)
Probabilistic model of influenza virus transmissibility at various temperature and humidity conditions
The spread efficiency of influenza virus is significantly affected by several environmental parameters. However, neither the underlying reasons, nor the exact character and magnitude of the phenomena involved are sufficiently well understood. Here we present a probabilistic approach to the virus transmission events. For a sample ensemble, we construct a… (More)
A model of influenza virus spread as a function of temperature and humidity
The influence that atmospheric conditions might have on the efficiency of the spread of influenza virus is important for epidemiological and evolutionary research. However, it has not been satisfactorily recognized and quantified so far. Here we provide a statistical model of influenza transmission between individuals. It has been derived from the results… (More)
Cellular & Molecular Biology Letters 603 Scc Dft-tb Energy Calculations of the Phosphoryl Transfer Reaction in the Pka Active Site
A self-consistent charge density-functional based tight binding method (SCC DFT TB) [1] is applied to study the phosphoryl-transfer reaction in the active site of protein kinase A (cAMP-dependent protein kinase). Test SCC-DFTB calculations for a model phosphoester system were compared with more advanced DFT B3LYP/6-31D+(d,p) calculations. It appeared that… (More)
Functional and effective brain connectivity for discrimination between Alzheimer's patients and healthy individuals: A study on resting state EEG rhythms.
OBJECTIVE This exploratory study provided a proof of concept of a new procedure using multivariate electroencephalographic (EEG) topographic markers of cortical connectivity to discriminate normal elderly (Nold) and Alzheimer's disease (AD) individuals. METHOD The new procedure was tested on an existing database formed by resting state eyes-closed EEG… (More)
A case study of software load balancing policies implemented with the PGAS programming model
Differential evolution algorithm was used to calculate the parameters C. Elegans connectome model. The calculations were carried out using the Java programming language coupled with PCJ library that enabled PGAS features within the JVM. The calculations clearly exhibited load imbalance, as some of the program's threads of execution were taking three times… (More)