Journal of Biological Physics

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A DNA-based in vitroGenetic Program
Journal of Biological Physics - Tập 28 - Trang 493-498 - 2002
J.A. Rose, M. Hagiya, R.J. Deaton, A. Suyama
In PNA-mediated Whiplash PCR (PWPCR), autonomous molecular computation is implemented by the recursive polymerase extension of a mixture of DNA hairpins. Like other methods based on exhaustive search, however, application to problem instances of realistic size is prevented by the exponential scaling of thesolution space. The tendency of evolving populations to minimize the sampling of large, low f... hiện toàn bộ
Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging
Journal of Biological Physics - Tập 39 - Trang 363-385 - 2013
A. G. Cherstvy, V. B. Teif
Chromatin domains formed in vivo are characterized by different types of 3D organization of interconnected nucleosomes and architectural proteins. Here, we quantitatively test a hypothesis that the similarities in the structure of chromatin fibers (which we call “structural homology”) can affect their mutual electrostatic and protein-mediated bridging interactions. For example, highly repetitive D... hiện toàn bộ
Stepwise oscillatory circuits of a DNA molecule
Journal of Biological Physics - Tập 35 - Trang 223-230 - 2009
Kunming Xu
A DNA molecule is characterized by a stepwise oscillatory circuit where every base pair is a capacitor, every phosphate bridge is an inductance, and every deoxyribose is a charge router. The circuitry accounts for DNA conductivity through both short and long distances in good agreement with experimental evidence that has led to the identification of the so-called super-exchange and multiple-step h... hiện toàn bộ
THz-Spectroscopy of Biological Molecules
Journal of Biological Physics - Tập 29 - Trang 89-100 - 2003
T.R. Globus, D.L. Woolard, T. Khromova, T.W. Crowe, M. Bykhovskaia, B.L. Gelmont, J. Hesler, A.C. Samuels
The terahertz frequency absorption spectraof DNA molecules reflect low-frequencyinternal helical vibrations involvingrigidly bound subgroups that are connectedby the weakest bonds, including thehydrogen bonds of the DNA base pairs,and/or non-bonded interactions. Althoughnumerous difficulties make the directidentification of terahertz phonon modes inbiological materials very challenging, ourresearc... hiện toàn bộ
Energy transport mechanism in the form of proton soliton in a one-dimensional hydrogen-bonded polypeptide chain
Journal of Biological Physics - Tập 42 - Trang 9-31 - 2015
L. Kavitha, R. Priya, N. Ayyappan, D. Gopi, S. Jayanthi
The dynamics of protons in a one-dimensional hydrogen-bonded (HB) polypeptide chain (PC) is investigated theoretically. A new Hamiltonian is formulated with the inclusion of higher-order molecular interactions between peptide groups (PGs). The wave function of the excitation state of a single particle is replaced by a new wave function of a two-quanta quasi-coherent state. The dynamics is governed... hiện toàn bộ
Biochemical oscillations and the development of organization
Journal of Biological Physics - Tập 10 - Trang 111-112 - 1982
Electrostatic potential comparison and molecular metric spaces
Journal of Biological Physics - - 1986
Ramon Carbot, Eduard Suñe, Felix Lapeña, Jose Perez
A possible definition of a metric associated with a set of electrostatic molecular potentials is analyzed. Examples of its application to formaldehyde and analogous structures, and to MAO substrates are presented.
Theoretical simulation of the calcium action potential in squid giant synapse: Repetitive stimulation
Journal of Biological Physics - Tập 19 - Trang 71-84 - 1993
Arunava Adhikari, Kamales Bhaumik
A biophysical model of the experimentally observed calcium action potential (CAP) in squid giant synapse is proposed. Whereas the inclusion of the inward calcium current in the Hodgkin-Huxley model can generate the rising phase of CAP, to account for the observed termination of the action potential, a repolarizing process needs to be introduced. Adding a term representing Ca-activated K current, t... hiện toàn bộ
Scaling of Folding Properties in Go Models of Proteins
Journal of Biological Physics - Tập 26 - Trang 273-294 - 2000
Marek Cieplak, Trinh Xuan Hoang
Insights about scaling of folding properties of proteins are obtained bystudying folding in heteropolymers described by Go-like Hamiltonians. Bothlattice and continuum space models are considered. In the latter case, themonomer-monomer interactions correspond to the Lennard-Jones potential.Several statistical ensembles of the two- and three-dimensional targetnative conformations are considered. Am... hiện toàn bộ
Enumerating Designing Sequences in the HP Model
Journal of Biological Physics - Tập 28 - Trang 1-15 - 2002
Anders Irbäck, Carl Troein
The hydrophobic/polar HP model on the square lattice has been widely used toinvestigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the number of contacts, the upper limit on the chain length N has been 18–20 because of the rapid exponential growth of thenumbers of conformations and sequences. W... hiện toàn bộ
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