Repository of works by Caltech published authors.
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Mostrando recursos 1 - 20 de 506
Virus-cell interaction with a tumor-producing virus - Vogt, Marguerite; Dulbecco, Renato
The polyoma(PY) virus or parotid tumor agent (1,2) -- a DNA-containing virus (3,4) -- is characterized by a duality of action: it produces neoplasias of various types in different species of rodents (5), and causes cell degeneration in mouse embryo tissue cultures (6). In the experiments to be reported here, it was possible to obtain in cellular cultures in vitro the oncogenic effect of the virus; this afforded the possibility of studying the relationship between the oncogenic and cytocidal effect of the virus. The results so far obtained reveal a situation novel in animal viruses and suggest the existence of...
Compensating impurity effect on epitaxial regrowth rate of amorphized Si - Suni, I.; Göltz, G.; Grimaldi, M. G.; Nicolet, M-A.; Lau, S. S.
The epitaxial regrowth of ion-implanted amorphous layers on <100> Si with partly compensated doping profiles of 11B, 75As, and 31P was studied. Single implants of these impurities are found to increase the regrowth rate at 475 and 500°C. The compensated layers with equal concentrations of 11B and 31P or 11B and 75As show a strong decrease of the regrowth whereas for the layers with overlapping 75As and 31P profiles no compensation has been found.
Decay of reactor neutrinos - Vogel, P.
We consider the decay of massive neutrinos which couple to electrons and are, therefore, produced in nuclear reactors. Lifetime limits for the γ and electron-positron decay modes of these neutrinos are deduced from the experimental limit on the singles count rate in the detector used to study neutrino oscillations at the Gösgen reactor. The dominantly coupled neutrinos are light, and their invariant-lifetime limit tc.m. / mν is 1-3 sec/eV. The subdominantly coupled heavy neutrinos with mass 1-4 MeV could decay into electron-positron pairs. These pairs were not observed, and from the absence of such a signal we deduce restrictions on...
Intercellular communication in normal and regenerating rat liver: a quantitative analysis - Meyer, David J.; Yancey, S. Barbara; Revel, Jean-Paul; Peskoff, Arthur
We have compared intercellular communication in the regenerating and normal livers of weanling rats. The electrophysiological studies were conducted at the edge of the liver, and we have found that here as elsewhere in the liver there is a dramatic decrease in the number and size of gap junctions during regeneration. The area of hepatocyte membrane occupied by gap junctions is reduced 100-fold 29-35 h after hepatectomy. By combining observations made with the scanning electron microscope with our freeze fracture data we have estimated the number of "communicating interfaces" (areas of contact between hepatocytes that include at least one gap...
v-abl causes hematopoietic disease distinct from that caused by bcr-abl - Scott, Martin L.; Van Etten, Richard A.; Daley, George Q.; Baltimore, David
v-abl, the oncogene transduced by Abelson murine leukemia virus, was first characterized by its ability to transform lymphoid cells. bcr-abl, the oncogene formed by a t(9;22) translocation thought to occur in human hematopoietic stem cells, is detectable in almost all cases of chronic myelogenous leukemia (CML), a malignancy of granulocytic cells. bcr-abl also causes a CML-like syndrome in mice whose bone-marrow cells are infected with a retrovirus transducing the gene. More recent reports have suggested that v-abl can, however, cause a disease similar to CML. We demonstrate here that v-abl, when transduced in a helper virus-containing system, causes disease similar...
Drift velocity of electrons in silicon at high electric fields from 4.2° to 300°K - Rodriguez, V.; Nicolet, M-A.
The drift velocity of electrons in silicon at high electric fields is measured in the <111> direction over the range of lattice temperatures from 4.2° to 300°K. It is established that in this range a limiting drift velocity exists. Its temperature dependence is measured. The samples used and the method of measurement are briefly described.
Symplectic quaternion scheme for biophysical molecular dynamics - Miller, T. F., III; Eleftheriou, M.; Pattnaik, P.; Ndirango, A.; Newns, D.; Martyna, G. J.
Massively parallel biophysical molecular dynamics simulations, coupled with efficient methods, promise to open biologically significant time scales for study. In order to promote efficient fine-grained parallel algorithms with low communication overhead, the fast degrees of freedom in these complex systems can be divided into sets of rigid bodies. Here, a novel Hamiltonian form of a minimal, nonsingular representation of rigid body rotations, the unit quaternion, is derived, and a corresponding reversible, symplectic integrator is presented. The novel technique performs very well on both model and biophysical problems in accord with a formal theoretical analysis given within, which gives an explicit...
Collision-induced conformational changes in glycine - Miller, Thomas F., III; Clary, David C.; Meijer, Anthony J. H.
We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes (III-->I and IV-->I), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters,...
Quantum free energies of the conformers of glycine on an ab initio potential energy surface - Miller, Thomas F., III; Clary, David C.
The torsional path integral Monte Carlo (TPIMC) technique is used to study the five lowest-energy conformers of glycine. The theoretical method provides an anharmonic and quantum-mechanical description of conformational free energy and is used for the first time with an ab initio potential energy surface. The 3-dimensional torsional potential energy surface of glycine was obtained at the MP2/6-311++G** level of theory and is optimized with respect to the non-torsional degrees of freedom. Calculated conformer populations compare well with those reported in recent matrix-isolation infrared spectroscopy experiments. An additional conformer, not yet observed, is predicted to be heavily populated in the...
Live Imaging at the Onset of Cortical Neurogenesis Reveals Differential Appearance of the Neuronal Phenotype in Apical versus Basal Progenitor Progeny - Attardo, Alessio; Calegari, Federico; Haubensak, Wulf; Wilsch-Bräuninger, Michaela; Huttner, Wieland B.
The neurons of the mammalian brain are generated by progenitors dividing either at the apical surface of the ventricular zone (neuroepithelial and radial glial cells, collectively referred to as apical progenitors) or at its basal side (basal progenitors, also called intermediate progenitors). For apical progenitors, the orientation of the cleavage plane relative to their apical-basal axis is thought to be of critical importance for the fate of the daughter cells. For basal progenitors, the relationship between cell polarity, cleavage plane orientation and the fate of daughter cells is unknown. Here, we have investigated these issues at the very onset of...
Torsional anharmonicity in the conformational thermodynamics of flexible molecules - Miller, Thomas F., III; Clary, David C.
We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of...
Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method - Nanjia, Shikha; Jasper, Ahren W.; Miller, Thomas F., III; Truhlar, Donald G.
The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for...
Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics - Miller, Thomas F., III; Manolopolous, David E.
We have used the ring-polymer molecular dynamics method to calculate approximate Kubo-transformed velocity autocorrelation functions and self-diffusion coefficients for low-pressure liquid para-hydrogen at temperatures of 25 and 14 K. The resulting diffusion coefficients are shown to be consistent with experimental shear viscosities and the established finite-size relation D(L)~=D([infinity])–2.837kBT/6pietaL, where kB is the Boltzmann constant, T the absolute temperature, eta the shear viscosity, and L the length of the (cubic) simulation cell. The diffusion coefficients D(L) obtained in simulations with finite system sizes are therefore too small. However, the extrapolation to infinite system size corrects this deficiency and leads to excellent...
Loss optimization of transverse Bragg resonance waveguides - Choi, John M.; Liang, Wei; Xu, Yong; Yariv, Amnon
Coupled-mode theory was used to analyze guiding in a transverse Bragg resonance (TBR) waveguide structure composed of a GaAs substrate with air holes. This analysis predicts that propagation loss will be minimized for discrete widths of the waveguide core. Although the coupled-mode theory is normally applied to structures with small index perturbations, two-dimensional finite-difference time-domain simulations of the TBR waveguide show good quantitative agreement with the coupled-mode predictions, and these results corroborate the previously predicted existence of discrete core widths for low-loss propagation.
A New Determination of e/m from the Zeeman Effect - Campbell, J. S.; Houston, W. V.
Values of e/m have been determined from the Zeeman separations of the Cd line 6439 and the Zn line 6362. For these lines the g-factors can be accurately determined from the theory. A magnetic field of 7300 gauss was produced by an air core solenoid in which the variation of field strength over a length of 6 cm at the center was less than 0.1 percent. The field to current ratio, K, of this solenoid was determined in terms of the calculated ratios of three single layer standard solenoids. The field strength during an exposure was then given by the...
Elastic constants of sodium from molecular dynamics - Çağin, Tahir; Ray, John R.
We have performed molecular-dynamics calculations of the adiabatic elastic constants of sodium at three different temperatures, T=198, 299, and 349 K. Our method uses fluctuation formulas appropriate for the microcanonical ensemble which contain the elastic constants. In the simulation we have used a first-principles potential to model the interaction between the sodium atoms. The results, including the shear modulus C44, show good agreement with experiment at all three temperatures. We have analyzed the contributions to the elastic constants from different types of terms appearing in the fluctuation formula and compared these contributions to other model-potential calculations. The volume dependence in...
Isothermal molecular-dynamics ensembles - Çağin, Tahir; Ray, John R.
S. Nosé [Mol. Phys. 52, 255 (1984); J. Chem. Phys. 81, 511 (1984)] has developed a form of molecular dynamics that generates the canonical ensemble. Since molecular-dynamics calculations are carried out at constant total linear momentum, we investigate the necessary modifications in Nosé’s theory when the constraint of constant total linear momentum is imposed. We show that Nosé’s theory can be modified so that it generates phase-space trajectories corresponding to a constant-momentum canonical ensemble with zero total momentum. We also present an exact treatment of the statistical mechanics of this constant-momentum canonical ensemble, including expressions relating averages to thermodynamic variables...
Fundamental treatment of molecular-dynamics ensembles - Çağin, Tahir; Ray, John R.
In microcanonical molecular dynamics the conservation of total momentum implies that the trajectories generate an ensemble with constant total momentum. We present the exact statistical mechanics of this microcanonical molecular dynamics ensemble. Using the adiabatic invariant phase volume to define the entropy, exact formulas, containing thermodynamic response functions, are derived for the microcanonical molecular dynamics ensemble and a numerical comparison of these formulas is made with fluctuation formulas which are valid in the thermodynamic limit and often used in molecular dynamics. No significant difference is found between the results calculated using the different formulas for a system of 432 particles;...
Inhibition of Carboxylase by Thiazole Pyrophosphate - Buchman, Edwin R.; Heegaard, Erik; Bonner, James
In the course of investigations dealing with vitamin B1 (thiamin) analogs, and having as their goal the furtherance of our knowledge of the physiological rôle of the vitamin, we have observed that a number of substances having a structure similar to that of cocarboxylase (thiamin pyrophosphate ), although not themselves able to replace the latter in the enzymatic decarboxylation of pyruvic acid, are able to inhibit markedly the activity of the carboxylase system. The most active inhibitant studied is the pyrophosphoric acid ester of the thiamin thiazole moiety (the thiazole pyrophosphate portion of the cocarboxylase molecule), which will be referred...
Is the Breakdown of the Born-Oppenheimer Approximation Responsible for Internal Conversion in Large Molecules? - Burland, D. M.; Robinson, G. W.
Vibronic radiationless transitions in large polyatomic molecules can be thought of as a process whereby the molecule, initially prepared in a discrete quasistationary state, makes a transition to an adjoining vibronic continuum belonging to a lower electronic state of the same multiplicity. In many instances the transition is analogous to penetration through a barrier between two "nested" potential sheets far away from an actual intersection of the sheets. Simultaneous distortions of vibrational and electronic parts of the wavefunction are required for such a tunneling process. The vibrational distortion manifests itself in the familiar Franck-Condon effect. The electronic distortion can be...