arXiv subjects

M. R. Ejtehadi

Publications and source records attributed to M. R. Ejtehadi.

25 records · Page 2Linked to original sources

arXiv2000

Geometry Selects Highly Designable Structures

By enumerating all sequences of length 20, we study the designability of structures in a two-dimensional Hydrophobic-Polar (HP) lattice model in a wide range of inter-monomer interaction parameters. We find that although the histogram of designability depends on interaction parameters, the set of highly designable structures is invariant. So in the HP lattice model the High Designability should be a purely geometrical feature. Our results suggest two geometrical properties for highly designable structures, they have maximum number of contacts and unique neighborhood vector representation. Also we show that contribution of perfectly stable sequences in designability of structures plays a major role to make them highly designable.

cond-mat.soft↗

arXiv1999

Protein Ground State Candidates in a Simple Model: An Exact Enumeration

The concept of the reduced set of contact maps is introduced. Using this concept we find the ground state candidates for Hydrophobic-Polar lattice model on a two dimensional square lattice. Using these results we exactly enumerate the native states of all proteins for a wide range of energy parameters. In this way, we show that there are some sequences, which have an absolute native state. Moreover, we study the scale-dependence of the number of the members of the reduced set, the number of ground state candidates, and the number of perfectly stable sequences by comparing the results for sequences with lengths of 6 up to 20.

cond-mat.soft↗

arXiv1998

Geometrically Reduced Number of Protein Ground State Candidates

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.

cond-mat.soft↗

arXiv1997

Highly Designable Protein Structures and Inter Monomer Interactions

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.

cond-mat.soft↗

arXiv1997

The field theory of Skyrme lattices in quantum Hall ferromagnets

We report the application of the nonlinear $σ$ model to study the multi-skyrmion problem in the quantum Hall ferromagnet system. We show that the ground state of the system can be described by a ferromagnet triangular Skyrme lattice near $ν=1$ where skyrmions are extremely dilute. We find a transition into antiferromagnet square lattice by increasing the skyrmion density and therefore $|ν-1|$. We investigate the possibility that the square Skyrme lattice deforms to a single skyrmion with the same topological charge when the Zeeman energy is extremely smaller than the Coulomb energy. We explicitly show that the energy of a skyrmion with charge two is less than the energy of two skyrmions each with charge one when $g \leq g_c$. By taking the quantum fluctuations into account, we also argue the possibility of the existence of a non-zero temperature Kosterlitz-Thouless and a superconductor-insulator phase transition.

cond-mat.mes-hall↗

arXiv1996

Shape Phase Transition of Polyampholytes in Two Dimensions

We have studied the transition in shape of two dimensional polyampholytes using Monte Carlo simulation. We observe that polymers with randomly charged monomers get into a globular shape at lower temperatures, provided that their total charge is below a critical value $Q_c$. Collapse into globular form happens for all forms of force law, but the critical charge depends on the form of the force law, inversely dependent on the range of interaction. The value of the critical charge is proportional to $N$, the size of the polymer, in the thermodynamic limit. PACS numbers: 36.20.-r, 35.20.Bm, 64.60.-i

cond-mat↗

arXiv1995

A model universe with variable dimension: Expansion as decrumpling

We propose a model universe, in which the dimension of the space is a continuous variable, which can take any real positive number. The dynamics leads to a model in which the universe has no singularity. The difference between our model and the standard Friedman-Robertson-Walker models become effective for times much before the presently accepted age of the universe.

gr-qc↗