Search results

1

Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

100%

Valenti D., Denaro G., Adorno D., Pizzolato N., Zammito S., Spagnolo B.

Open Physics

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2012

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vol. 10

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issue 3

560-567

EN

Polymer translocation through the nanochannel is studied by means of a Monte Carlo approach, in the presence of a static or oscillating external electric voltage. The polymer is described as a chain molecule according to the two-dimensional “bond fluctuation model”. It moves through a piecewise linear channel, which mimics a nanopore in a biological membrane. The monomers of the chain interact with the walls of the channel, modelled as a reflecting barrier. We analyze the polymer dynamics, concentrating on the translocation time through the channel, when an external electric field is applied. By introducing a source of coloured noise, we analyze the effect of correlated random fluctuations on the polymer translocation dynamics.

2

First steps toward the construction of a hyperphase diagram that covers different classes of short polymer chains

100%

Sabeur S.

Open Physics

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2014

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vol. 12

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issue 6

421-426

EN

We present the results of a multicanonical Monte Carlo study of flexible and wormlike polymer chains, where we investigate how the polymer structures observed during the simulations, mainly coil, liquid, and crystalline structures, can help to construct a hyperphase diagram that covers different polymer classes according to their thermodynamic behavior.

3

Monte Carlo study on bilayer thin films magnetic properties dependence with discontinouos anisotropy parameters

100%

Bîrsan E.

Open Physics

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2008

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vol. 6

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issue 2

296-305

EN

In the last few years there has been significant interest in the field of thin films, due to numerous specific phenomena related to the low dimension of these systems, and to the large opportunities in development of high technologies based on their specific magnetic and electronic properties. When dealing with systems of reduced dimensionality it is important to take into account the influence of magnetic anisotropies. In this paper we investigate the magnetic properties of bilayer thin film. This behavior is modeled using Monte Carlo simulations, in the Extended Anisotropic Heisenberg Model. The magnetization, out-of-plane and in-plane magnetic susceptibilities, and also the specific heat bearings according to temperature are investigated in order to find the potential magnetic ordering phases and the critical temperatures, for two sets parameter assignments. For quasi-uniform anisotropy parameters of the film we detect the ferromagnetism-paramagnetism transition and then, by changing the model parameters values, we relieve a short range ferromagnetic ordering phase arising from the antiferromagnetic base layer coupling influence and from easy-plane anisotropy discontinuity on the layers interface.

4

The zone strong coupling two-channel totally asymmetric simple exclusion processes

100%

Xiao S., Tang L., Wang H.

Open Physics

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2011

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vol. 9

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issue 4

1077-1083

EN

This article investigates the zone strong coupling two-channel totally asymmetric simple exclusion processes (TASEPs). The study is based on Pronina and Kolomeisky’s work [J. Phys. A-Math. Gen. 37, 9907 (2004)], in which the coupling exists within two whole parallel channels. Zone strong coupling two-channel TASEPs focuses on the behavior and the effect of a particular segment rather than the whole channel. The study shows that there are five possible stationary phases; LD/LD, HD/HD, MC/LD, LD/HD, and MC/HD. The phase diagrams and the density profiles are investigated using computer Monte Carlo simulations and mean-field approximation. The outcomes of the simulations match agreeably with the analytical predictions.

5

Simulation of dissociation of DNA duplexes attached to the surface

100%

Zhdanov V., Gunnarsson A., Höök F.

Open Physics

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2010

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vol. 8

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issue 6

883-892

EN

We present Monte Carlo simulations of dissociation of duplexes formed of complementary single-stranded DNAs with one of the strands attached to the surface. To describe the transition from the bound state to the unbound state of two strands located nearby, we use a lattice model taking DNA base-pair interactions and comformational changes into account. The results obtained are employed as a basis for a more coarse-grained model including strand backward association and diffusion resulting in complete dissociation. The distribution of the dissociation time is found to be exponential. This finding indicates that the non-exponential kinetic features observed in the corresponding experiments seem to be related to extrinsic factors, e.g., to the surface heterogeneity.

6

Protein modeling and structure prediction with a reduced representation.

88%

Kolinski A.

Acta Biochimica Polonica

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2004

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vol. 51

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issue 2

349-371

EN

Protein modeling could be done on various levels of structural details, from simplified lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular mechanics. Here I describe a new high resolution reduced model, its force field and applications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sampling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic protein-like conformational biases, statistical potentials for the short-range conformational propensities, a model of the main chain hydrogen bonds and context-dependent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.

7

TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling

88%

Trojanowski S., Rutkowska A., Kolinski A.

Acta Biochimica Polonica

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2010

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vol. 57

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issue 1

125-133

EN

A new approach to comparative modeling of proteins, TRACER, is described and benchmarked against classical modeling procedures. The new method unifies true three-dimensional threading with coarse-grained sampling of query protein conformational space. The initial sequence alignment of a query protein with a template is not required, although a template needs to be somehow identified. The template is used as a multi-featured fuzzy three-dimensional scaffold. The conformational search for the query protein is guided by intrinsic force field of the coarse-grained modeling engine CABS and by compatibility with the template scaffold. During Replica Exchange Monte Carlo simulations the model chain representing the query protein finds the best possible structural alignment with the template chain, that also optimizes the intra-protein interactions as approximated by the knowledge based force field of CABS. The benchmark done for a representative set of query/template pairs of various degrees of sequence similarity showed that the new method allows meaningful comparative modeling also for the region of marginal, or non-existing, sequence similarity. Thus, the new approach significantly extends the applicability of comparative modeling.

8

Numerical study of the three-state Ashkin-Teller model with competing dynamics

88%

Ndizeye P., Hontinfinde F., Kounouhewa B., Bekhechi S.

Open Physics

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2014

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vol. 12

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issue 5

375-382

EN

An open ferromagnetic Ashkin-Teller model with spin variables 0, ±1 is studied by standard Monte Carlo simulations on a square lattice in the presence of competing Glauber and Kawasaki dynamics. The Kawasaki dynamics simulates spin-exchange processes that continuously flow energy into the system from an external source. Our calculations reveal the presence, in the model, of tricritical points where first order and second order transition lines meet. Beyond that, several self-organized phases are detected when Kawasaki dynamics become dominant. Phase diagrams that comprise phase boundaries and stationary states have been determined in the model parameters’ space. In the case where spin-phonon interactions are incorporated in the model Hamiltonian, numerical results indicate that the paramagnetic phase is stabilized and almost all of the self-organized phases are destroyed.

9

Protein modeling with reduced representation: statistical potentials and protein folding mechanism

75%

Ekonomiuk D., Kielbasinski M., Andrzej K.

Acta Biochimica Polonica

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2005

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vol. 52

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issue 4

741-748

EN

A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon β-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the β-sheet.

10

Multi-stage analysis of reliability of an example masonry construction

75%

Zięba J., Buda-Ożóg L., Skrzypczak I., Zięba J., Buda-Ożóg L., Skrzypczak I.

Archives of Civil Engineering

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2021

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vol. 67

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issue 2

Refine search results

Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

First steps toward the construction of a hyperphase diagram that covers different classes of short polymer chains

Monte Carlo study on bilayer thin films magnetic properties dependence with discontinouos anisotropy parameters

The zone strong coupling two-channel totally asymmetric simple exclusion processes

Simulation of dissociation of DNA duplexes attached to the surface

Protein modeling and structure prediction with a reduced representation.

TRACER. A new approach to comparative modeling that combines threading with free-space conformational sampling

Numerical study of the three-state Ashkin-Teller model with competing dynamics

Protein modeling with reduced representation: statistical potentials and protein folding mechanism

Multi-stage analysis of reliability of an example masonry construction