Biology

Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

Robert A. Latour
While the importance of protein adsorption to materials surfaces is widely recognized, little is understood at this time regarding how to design surfaces to control protein adsorption behavior. All-atom empirical force field molecular simulation methods have enormous potential to address this proble ... [Biointerphases 3, FC2 (2008)] published Thu Sep 4, 2008.

Electrochemical switching of the flavoprotein dodecin at gold surfaces modified by flavin-DNA hybrid linkers

Martin Grininger, Gilbert Noll, Sibylle Trawoger, Eva-Kathrin Sinner, and Dieter Oesterhelt
Dodecin from Halobacterium salinarum is a dodecameric, hollow-spherical protein, which unspecifically adopts flavin molecules. Reduction of flavin dodecin holocomplexes induces dissociation into apododecin and free flavin. Unspecific binding and dissociation upon reduction were used as key propertie ... [Biointerphases 3, 51 (2008)] published Thu Sep 4, 2008.

Multiple impact regimes in liquid environment dynamic atomic force microscopy

John Melcher, Xin Xu, and Arvind Raman
A canonical assumption in dynamic atomic force microscopy is that the probe tip interacts with the sample once per oscillation cycle. We show this key ansatz breaks down for soft cantilevers in liquid environments. Such probes exhibit drum roll like dynamics with sequential bifurcations between osci ... [Appl. Phys. Lett. 93, 093111 (2008)] published Thu Sep 4, 2008.

Near-field radiative heat transfer between a sphere and a substrate

Arvind Narayanaswamy, Sheng Shen, and Gang Chen
Near-field force and energy exchange between two objects due to quantum electrodynamic fluctuations give rise to interesting phenomena such as Casimir and van der Waals forces and thermal radiative transfer exceeding Planck's theory of blackbody radiation. Although significant progress has been made ... [Phys. Rev. B 78, 115303 (2008)] published Thu Sep 4, 2008.

Amide-I relaxation-induced hydrogen bond distortion: An intermediate in electron capture dissociation mass spectrometry of alpha-helical peptides?

Vincent Pouthier and Yury O. Tsybin
Electron capture dissociation (ECD) of peptides and proteins in the gas phase is a powerful tool in tandem mass spectrometry whose current description is not sufficient to explain many experimental observations. Here, we attempt to bridge the current understanding of the vibrational dynamics in alph ... [J. Chem. Phys. 129, 095106 (2008)] published Thu Sep 4, 2008.

Synthesis of a Pattern Generation Mechanism for Gait Rehabilitation

Zhiming Ji and Yazan Manna
Gait training is a major part of neurological rehabilitation. Robotic gait training systems provide paraplegic patients with consistent, labor-saving, and adjustable physical therapy over traditional manual trainings. However the high cost and social-technical concerns on safe operation currently li ... [J. Med. Devices 2, 031004 (2008)] published Thu Sep 4, 2008.

An Infant Surgical Table for Laser Photocoagulation: Design and Development

Kimberly Ryland, Carl A. Nelson, and Thomas Hejkal
Retinopathy of prematurity, caused by abnormal blood vessel development in the retina of premature infants, is a leading cause of childhood blindness. It is treated using laser photocoagulation. Current methods require the surgeon to assume awkward standing positions, which can result in injury to t ... [J. Med. Devices 2, 031003 (2008)] published Thu Sep 4, 2008.

Monitoring the Bragg peak location of 73 MeV/u carbon ions by means of prompt gamma-ray measurements

E. Testa, M. Bajard, M. Chevallier, D. Dauvergne, F. Le Foulher et al.
By means of a time-of-flight technique, we measured the longitudinal profile of prompt gamma-rays emitted by 73 MeV/u C ions irradiating a polymethyl methacrylate target. This technique allowed us to minimize the shielding against neutrons and scattered gamma-rays, and to correlate prompt gamma emi ... [Appl. Phys. Lett. 93, 093506 (2008)] published Wed Sep 3, 2008.

Toward a thermodynamically consistent picture of the phase-field model of vesicles: Curvature energy

D. Jamet and C. Misbah
We extend our recent work on phase-field model for vesicles [D. Jamet and C. Misbah, Phys. Rev. E 76, 051907 (2007)]where only the membrane local incompressibility was treatedto the situation where the bending forces and spontaneous curvature are included. We show how the general phase-field equatio ... [Phys. Rev. E 78, 031902 (2008)] published Wed Sep 3, 2008.

Influence of correlations on molecular recognition

Hans Behringer and Friederike Schmid
The influence of the patchiness and correlations in the distribution of hydrophobic and polar residues at the interface between two rigid biomolecules on their recognition ability is investigated in idealized coarse-grained lattice models. A general two-stage approach is utilized where an ensemble o ... [Phys. Rev. E 78, 031903 (2008)] published Wed Sep 3, 2008.

Ab initio determination of the electron affinities of DNA and RNA nucleobases

Daniel Roca-Sanjuan, Manuela Merchan, Luis Serrano-Andres, and Mercedes Rubio
High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the ... [J. Chem. Phys. 129, 095104 (2008)] published Wed Sep 3, 2008.

Electronic state of iron in enterobactin using M[o-umlaut]ssbauer spectroscopy

K. Spartalian, W. T. Oosterhuis, and J. B. Neilands
Well-resolved paramagnetic hyperfine structure is observed in the Mossbauer spectra of Fe complexed by enterobactin, an iron transport compound found in many enteric bacteria. Spectra were observed under varied conditions of temperature (4.277 K) and applied magnetic field (06 kOe). The spectra for ... [J. Chem. Phys. 62, 3538 (2008)] published Wed Sep 3, 2008.

[sup 25]Mg and [sup 14]N nuclear quadrupole resonances in chlorophyll-a and magnesium phthalocyanine

O. Lumpkin
Mg and N zero field nuclear quadrupole resonance are observed in chlorophyll-a and magnesium phthalocyanine by proton nuclear magnetic double resonance. In phthalocyanine, the observed resonances correspond to a quadrupole coupling constant of 3.79 MHz for Mg and 1.81 MHz for the N ligands. In chlor ... [J. Chem. Phys. 62, 3281 (2008)] published Wed Sep 3, 2008.

M[o-umlaut]ssbauer studies of Fe[sup 2 + ] in anhydrous hemoglobin and its isolated subunits

G. C. Papaefthymiou, B. H. Huynh, C. S. Yen, J. L. Groves, and C. S. Wu
The Mossbauer spectra of dehydrated alpha and beta deoxyhemoglobin subunits were obtained over a temperature range from 77 to 200 degrees K and compared with anhydrous hemoglobin spectra. The Mossbauer data for both subunits show a superposition of a ferrous high spin (S = 2) and a ferrous low spin ... [J. Chem. Phys. 62, 2995 (2008)] published Wed Sep 3, 2008.

A short range probe for investigating metalloprotein structures: Fourier analysis of the extended x-ray absorption fine structure

D. E. Sayers, F. W. Lytle, M. Weissbluth, and P. Pianetta
... [J. Chem. Phys. 62, 2514 (2008)] published Wed Sep 3, 2008.

Some models for lipid bilayer and biomembrane phase transitions

H. L. Scott, Jr.
Biological membranes consist to a large extent of lipid bilayers, some of which exhibit fairly sharp phase transitions near body temperatures. We describe here a model for the main observed phase transition in pure lipid monolayers and bilayers. The model contains approximate treatments of hardcore ... [J. Chem. Phys. 62, 1347 (2008)] published Wed Sep 3, 2008.

Polarized Raman scattering from a helical biopolymer

W. T. Wilser and D. B. Fitchen
Polarized Raman spectra are reported for thin films of oriented alphahelices of polygammabenzyllglutamate. All four independent spectra were measured using 180 degrees scattering at nearnormal incidence and 90 degrees scattering at grazing incidence. Polarization ratios are analyzed in terms of sc ... [J. Chem. Phys. 62, 720 (2008)] published Wed Sep 3, 2008.

Resonance Raman spectra of Cu-etioporphyrins I, I-meso-d[sub 4], and IV

R. Mendelsohn, S. Sunder, A. L. Verma, and H. J. Bernstein
Resonance Raman spectra obtained using the Ar and tunable Rhodamine 6G dye lasers are presented for the position isomers Cuetioporphyrin I and IV in dilute (10 M) solution. The spectra show significant differences in several vibrations enabling the molecules to be distinguished. Several anomalously ... [J. Chem. Phys. 62, 37 (2008)] published Wed Sep 3, 2008.

Coherence, collective rhythm, and phase difference distribution in populations of stochastic genetic oscillators with cellular communication

Zhanjiang Yuan, Jiajun Zhang, and Tianshou Zhou
An ensemble of stochastic genetic relaxation oscillators via phase-attractive or repulsive cell-to-cell communication are investigated. In the phase-attractive coupling case, it is found that cellular communication can enhance self-induced stochastic resonance as well as collective rhythms, and that ... [Phys. Rev. E 78, 031901 (2008)] published Tue Sep 2, 2008.

Polarization-dependent fluorescence of proteins bound to nanopore-confined lipid bilayers

R.-Q. Li, A. Marek, Alex I. Smirnov, and H. Grebel
Lipid bilayers are essential structural component of biological membranes of all the living species: from viruses and bacteria to plants and humans. Biophysical and biochemical properties of such membranes are important for understanding physical mechanisms responsible for drug targeting. Binding ev ... [J. Chem. Phys. 129, 095102 (2008)] published Tue Sep 2, 2008.

Three-dimensional orientation determination of the emission dipoles of single molecules: The shot-noise limit

Johannes Hohlbein and Christian G. Hubner
The power of three-dimensional orientation detection of single emitting dipoles using a sophisticated scheme with three detectors in a confocal microscope is quantitatively explored by means of Monte Carlo simulations. We show that several hundreds of photons are sufficient for a reliable orientatio ... [J. Chem. Phys. 129, 094703 (2008)] published Tue Sep 2, 2008.

Generating properly weighted ensemble of conformations of proteins from sparse or indirect distance constraints

Ming Lin, Hsiao-Mei Lu, Rong Chen, and Jie Liang
Inferring three-dimensional structural information of biomacromolecules such as proteins from limited experimental data is an important and challenging task. Nuclear Overhauser effect measurements based on nucleic magnetic resonance, disulfide linking, and electron paramagnetic resonance labeling st ... [J. Chem. Phys. 129, 094101 (2008)] published Tue Sep 2, 2008.

High precision capacitance bridge for studying lipid bilayer membranes

Stephen H. White and David N. Blessum
A simple ac bridge for the measurement of the capacitance of lipid bilayer membranes between 100 Hz and 10 kHz with a nominal accuracy of about 0.1% without corrections is described. The voltage across the unknown need be only 7 mV (rms). Using a simple calibration procedure, the capacitance can be ... [Rev. Sci. Instrum. 46, 1462 (2008)] published Tue Sep 2, 2008.

Portable, solid-state fluorometer for the measurement of chlorophyll fluorescence induction in plants

Ulrich Schreiber, Leslie Groberman, and William Vidaver
A miniaturized Kautsky apparatus was developed for measuring chlorophyll fluorescence induction in photosynthetic plants in situ. The instrument is based on a new sensoremitter combination of a phototransistor on the back of a light emitting diode (piggy-back arrangement). Fluorescence curves can be ... [Rev. Sci. Instrum. 46, 538 (2008)] published Tue Sep 2, 2008.

Machine for rapidly counting and measuring the size of small nematodes

L. Byerly, R. C. Cassada, and R. L. Russell
A machine has been developed to accurately count and size large populations of the small nematode Caenorhabditis elegans with minimal effort. Like the related Coulter counter, this machine detects the change in electrical current which a particle (nematode) produces as it passes between two electrod ... [Rev. Sci. Instrum. 46, 517 (2008)] published Tue Sep 2, 2008.

Variable frequency exposure system for small biological specimens

D. McRee, P. Walsh, and R. Mathew
A variable frequency microwave exposure system for use in the study of the bioeffects of cw and frequency modulated radiation has been designed, built, and calibrated. The frequency range of the system is 110 GHz. The power density range at the specimen location for all the specified frequencies is ... [Rev. Sci. Instrum. 46, 253 (2008)] published Tue Sep 2, 2008.

High pressure optical cell for biochemical studies

Richard Kenneth Williams
The adaptation of a commercially available high pressure optical cell to monitor changes in absorbance in aqueous solutions by use of a fused quartz cuvette, and a high pressure seal, inert to nhexane, is described. Measurements of percent transmittance to an accuracy of 0.2% have been obtained. Con ... [Rev. Sci. Instrum. 46, 250 (2008)] published Tue Sep 2, 2008.

AES analysis of sodium in a corroded bioglass using a low-temperature technique

C. G. Pantano Jr., D. B. Dove, and G. Y. Onoda Jr.
Measurements have been made of sodium compositional profiles at a glass surface using Auger electron spectroscopy. It has been found that stable sodium signals may be obtained by lowering the temperature of the glass to 80 degrees K and by keeping the exciting electron beam current to less than 1 [ ... [Appl. Phys. Lett. 26, 601 (2008)] published Tue Sep 2, 2008.

Pulse propagation on a superconductive neuristor

Stanley A. Reible and Alwyn C. Scott
Both analytic study and experimental investigations on an electronic analog are presented which indicate the unstable nature of Parmentier's traveling-wave pulse on a superconductive neuristor. In the vicinity of a critical bias level, the pulse is almost stable in the sense that pulse distortion ov ... [J. Appl. Phys. 46, 4935 (2008)] published Tue Sep 2, 2008.

Monte Carlo treatment of multiple Coulomb scattering in pion-beam dose calculations

R. N. Hamm, H. A. Wright, and J. E. Turner
Multiple scattering of negative pions in tissue is investigated by Monte Carlo methods for an 82-MeV pencil beam by using (i) single deflections of each pion at the target surface with straight trajectories thereafter, (ii) successive angular deflections after specified distances of travel in the ta ... [J. Appl. Phys. 46, 4445 (2008)] published Tue Sep 2, 2008.

Current-fluctuation noise in toad urinary bladder during active transport of sodium ions

M. W. P. Strandberg and Earle I. Hammer
The voltage-fluctuation noise spectrum appearing across the excised urinary bladder of the female Dominican toad Bufo marinus during active transport of sodium is identified as arising from random current fluctuations in the sodium-ion active transport current. The noise is observed to disappear wit ... [J. Appl. Phys. 46, 3661 (2008)] published Tue Sep 2, 2008.

Contribution of active transport current to the effective membrane impedance

M. W. P. Strandberg
It is shown that a membrane which supports active transport of ions will have an impedance which differs from that represented by the passive distributed resistance and capacitance (1) if the active transport current magnitude varies with transmembrane potential and (2) if the active transport curre ... [J. Appl. Phys. 46, 3654 (2008)] published Tue Sep 2, 2008.

Measurements of SO[sub 2] absorption coefficients using a tunable dye laser

R. T. Thompson Jr., J. M. Hoell Jr., and W. R. Wade
High-resolution measurements of SO absorption coefficients in the uv are presented in the wavelength interval between 2962 and 3011 A using a frequency-doubled dye laser as the radiation source. These measurements have application to pollution monitoring of SO using the differential absorption scatt ... [J. Appl. Phys. 46, 3040 (2008)] published Tue Sep 2, 2008.

Calibrated remote measurements of SO[sub 2] and O[sub 3] using atmospheric backscatter

W. B. Grant and R. D. Hake Jr.
Remote measurements of calibrated samples of SO and O have been achieved with a lidar using ultraviolet signals produced by a tunable dye laser and a nonlinear crystal. The operating wavelengths for these measurements were 292.3 and 293.3 nm for SO and 292.3 and 294.0 nm for O. The atmosphere in fro ... [J. Appl. Phys. 46, 3019 (2008)] published Tue Sep 2, 2008.

Fluorescence tomography technique optimized for noninvasive imaging of the mouse brain

Riad Bourayou, Heide Boeth, Heval Benav, Thomas Betz, Ute Lindauer et al.
In vivo molecular fluorescence tomography of brain disease mouse models has two very specific demands on the optical setup: the use of pigmented furry mice does not allow for a purely noncontact setup, and a high spatial accuracy is required on the dorsal side of the animal due to the location of th ... [J. Biomed. Opt. 13, 041311 (2008)] published Fri Aug 29, 2008.

Intravital high-resolution optical imaging of individual vessel response to photodynamic treatment

Mamta Khurana, Eduardo H. Moriyama, Adrian Mariampillai, and Brian C. Wilson
Intravital imaging using confocal microscopy facilitates high-resolution studies of cellular and molecular events in vivo. We use this, complemented by Doppler optical coherence tomography (OCT), to assess blood flow in a mouse dorsal skin-fold window chamber model to image the response of individua ... [J. Biomed. Opt. 13, 040502 (2008)] published Fri Aug 29, 2008.

Diffuse spectral fundus reflectance measured using subretinally placed spectralon

David A. Salyer, Kurt R. Denninghoff, Neil Beaudry, Sreenivasa Basavanthappa, Robert I. Park et al.
The diffuse fundus reflectance and the spectral transmittance of the swine sensory retina was measured in vivo using intravitreal illumination. Pars plana vitrectomy and intravitreal manipulations were performed on a female American Yorkshire domestic swine. Light from a scanning monochromator was c ... [J. Biomed. Opt. 13, 044004 (2008)] published Fri Aug 29, 2008.

Implementation of IAEA /1/INT/054 Project in Nuclear Analytical Techniques Group of Argentina: Current State

Resnizky Sara, Pla Rita, and Zaretzky Alba
This paper presents the implementation of the training received through the IAEA Project Preparation of Reference Materials and Organization of Proficiency Tests Rounds in the Nuclear Analytical (NAT) Group of CNEA. Special emphasis is done on those activities related to the first Proficiency Test b ... [AIP Conf. Proc. 1036, 63 (2008)] published Fri Aug 29, 2008.

Quantum Monte Carlo study of porphyrin transition metal complexes

Jun Koseki, Ryo Maezono, Masanori Tachikawa, M. D. Towler, and R. J. Needs
Diffusion quantum Monte Carlo (DMC) calculations for transition metal (M) porphyrin complexes (MPo, M=Ni,Cu,Zn) are reported. We calculate the binding energies of the transition metal atoms to the porphin molecule. Our DMC results are in reasonable agreement with those obtained from density function ... [J. Chem. Phys. 129, 085103 (2008)] published Fri Aug 29, 2008.

Solutions of the Maxwell viscoelastic equations for displacement and stress distributions within the arterial wall

S. Hodis and M. Zamir
Mechanical events within the thickness of the vessel wall caused by pulsatile blood flow are considered, with focus on axial dynamics of the wall, driven by the oscillatory drag force exerted by the fluid on the endothelial layer of the wall. It is shown that the focus on the axial direction makes i ... [Phys. Rev. E 78, 021914 (2008)] published Fri Aug 29, 2008.

Characterization of multiple spiral wave dynamics as a stochastic predator-prey system

Niels F. Otani, Alisa Mo, Sandeep Mannava, Flavio H. Fenton, Elizabeth M. Cherry et al.
A perspective on systems containing many action potential waves that, individually, are prone to spiral wave breakup is proposed. The perspective is based on two quantities, predator and prey, which we define as the fraction of the system in the excited state and in the excitable but unexcited state ... [Phys. Rev. E 78, 021913 (2008)] published Fri Aug 29, 2008.

High throughput system for magnetic manipulation of cells, polymers, and biomaterials

Richard Chasen Spero, Leandra Vicci, Jeremy Cribb, David Bober, Vinay Swaminathan et al.
In the past decade, high throughput screening (HTS) has changed the way biochemical assays are performed, but manipulation and mechanical measurement of micro- and nanoscale systems have not benefited from this trend. Techniques using microbeads (particles ~0.110 [mu]m) show promise for enabling hi ... [Rev. Sci. Instrum. 79, 083707 (2008)] published Fri Aug 29, 2008.

Numerical Simulations of Flow in Cerebral Aneurysms: Comparison of CFD Results and In Vivo MRI Measurements

Vitaliy L. Rayz, Loic Boussel, Gabriel Acevedo-Bolton, Alastair J. Martin, William L. Young et al.
Computational fluid dynamics (CFD) methods can be used to compute the velocity field in patient-specific vascular geometries for pulsatile physiological flow. Those simulations require geometric and hemodynamic boundary values. The purpose of this study is to demonstrate that CFD models constructed ... [J. Biomech. Eng. 130, 051011 (2008)] published Fri Aug 29, 2008.

Interfacial adsorption and denaturization of human milk and recombinant rice lactoferrin

Fang Pan, XiuBo Zhao, Thomas A. Waigh, Jian R. Lu, and Fausto Miano
Lactoferrin (LF) produced from recombinant technologies can achieve almost identical amino acid sequences and three-dimensional structures to those extracted from mammals, but differences often arise in the carbohydrate chains attached through N-glycosylation, with altered sizes, structures, and che ... [Biointerphases 3, FB36 (2008)] published Fri Aug 29, 2008.

Repulsion Between Inorganic Particles Inserted Within Surfactant Bilayers

Doru Constantin, Brigitte Pansu, Marianne Imperor, Patrick Davidson, and Francois Ribot
We study by synchrotron small-angle x-ray scattering highly aligned lamellar phases of a zwitterionic surfactant, doped with monodisperse and spherical hydrophobic inorganic particles as a function of particle concentration. Analysis of the structure factor of the two-dimensional fluid formed by the ... [Phys. Rev. Lett. 101, 098101 (2008)] published Fri Aug 29, 2008.

Two-moment characterisation of subcellular biochemical networks: when noise matters. (arXiv:0809.0773v1 [q-bio.SC])

ePrint arXiv http://arXiv.org/

On the application of the variational iteration method to a prey and predator model with variable coefficients. (arXiv:0808.1875v2 [math-ph] UPDATED)

ePrint arXiv http://arXiv.org/