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J. García de la Torre

Bio: J. García de la Torre is an academic researcher from University of Murcia. The author has contributed to research in topics: Brownian dynamics & Shear flow. The author has an hindex of 28, co-authored 99 publications receiving 3787 citations.


Papers
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Journal ArticleDOI
TL;DR: The ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, is extended to models with lower, residue-level resolution, allowing calculations when atomic resolution is not available or coarse-grained models are preferred.

602 citations

Journal ArticleDOI
TL;DR: A computational procedure to calculate the rotational diffusion tensor and other properties of proteins from their detailed, atomic-level structure, using bead models for prediction of hydrodynamic properties of arbitrarily shaped particles.

521 citations

Journal ArticleDOI
TL;DR: HYDRO is a program for the calculation of sedimentation and diffusion coefficients, rotational relaxation times, and intrinsic viscosities of rigid macromolecules of arbitrary shape that are represented by bead models.

287 citations

Journal ArticleDOI
TL;DR: In this paper, the hydrodynamic properties of cylindrical (rodlike and discoidal) particles in dilute solution have been computed using the bead-shell model treatment.
Abstract: The hydrodynamic properties of cylindrical (rodlike and discoidal) particles in dilute solution have been computed using the bead-shell model treatment. Previous results [Tirado and Garcia de la Torre, J. Chem. Phys. 71, 2581 (1979); 73, 1993 (1980)] for rods with length-to-diameter ratio p>2 are now extended to short cylinders and disks down to p=0.1. The intrinsic viscosity is obtained for rods and disks, and results are presented for the three rotational relaxation times of a cylindrical particle. The hydrodynamic properties are expressed in forms that have a weak variation with p, and are therefore useful for the analysis of experimental values. We present examples of the determination of the length and diameter of the cylindrical particles, for DNA oligonucleotides and tobacco mosaic virus.

272 citations

Journal ArticleDOI
TL;DR: It is found how a correction due to the nonzero volume of the beads can be estimated from the geometry of the model, and its application yields results that are within the range of typical experimental errors.
Abstract: The conventional Kirkwood-Riseman calculation of the hydrodynamic properties of bead models gives abnormal results for rotational quantities and the intrinsic viscosities for models with a few beads or when one bead is dominant. The reason is that beads are treated as point sources of friction. This can be remedied by introducing terms that are neglected in the conventional treatment of orders 0 and -3 in interbead distances. An alternative strategy is the cubic substitution in which each bead is replaced by a cubic array of minibeads. These procedures require a computational overload that, in the case of the intrinsic viscosity, can be avoided using an estimate of the correction due to the nonzero volume of the beads. We have found how such a correction can be estimated from the geometry of the model, and its application yields results that are within the range of typical experimental errors.

148 citations


Cited by
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Journal ArticleDOI
01 Apr 1988-Nature
TL;DR: In this paper, a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) is presented.
Abstract: Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

9,929 citations

Journal ArticleDOI
TL;DR: This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level, including the Perrin equation, based on the measured sedimentation coefficient and the calculated maximum S to estimate if a protein is globular or elongated.
Abstract: An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. A combination of hydrodynamics and electron microscopy is especially powerful.

1,308 citations

Journal ArticleDOI
TL;DR: A survey of the classical works in mechanochemistry is given and the key mechanochemical phenomena into perspective with recent results from atomic force microscopy and quantum molecular dynamics simulations are put into perspective.
Abstract: Regarding the activation of chemical reactions, today’s chemist is used to thinking in terms of thermochemistry, electrochemistry, and photochemistry, which is reflected in the organization and content of the standard physical chemistry textbooks. The fourth way of chemical activation, mechanochemistry, is usually less well-known. The purpose of the present review is to give a survey of the classical works in mechanochemistry and put the key mechanochemical phenomena into perspective with recent results from atomic force microscopy and quantum molecular dynamics simulations. A detailed historical account on the development of mechanochemistry, with an emphasis on the mechanochemistry of solids, was recently given by Boldyrev and Tkáčová.1 The first written document of a mechanochemical reaction is found in a book by Theophrastus of Ephesus (371-286 B.C.), a student of Aristotle, “De Lapidibus” or “On stones”. If native cinnabar is rubbed in a brass mortar with a brass pestle in the presence of vinegar, metallic mercury is obtained. The mechanochemical reduction probably follows the reaction:1-3 * To whom correspondence should be addressed. Telephone: ++49-89-289-13417. Fax: ++49-89-289-13416. E-mail: martin.beyer@ch.tum.de (M.K.B.); Telephone: ++49-89-12651417. Fax: ++49-89-1265-1480. E-mail: clausen-schaumann@ fhm.edu (H.C.-S.). † Technische Universität München. ‡ Institut für Strahlenschutz. § Current address: Munich University of Applied Sciences. HgS + Cu f Hg + CuS (1) Volume 105, Number 8

1,062 citations

Journal ArticleDOI
TL;DR: The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in the previous article, using a HYDROPRO public-domain computer program.

1,058 citations

Journal ArticleDOI
06 Dec 2007-Nature
TL;DR: It is shown that pico- to nano-second timescale atomic fluctuations in hinge regions of adenylate kinase facilitate the large-scale, slower lid motions that produce a catalytically competent state.
Abstract: The synergy between structure and dynamics is essential to the function of biological macromolecules. Thermally driven dynamics on different timescales have been experimentally observed or simulated, and a direct link between micro- to milli-second domain motions and enzymatic function has been established. However, very little is understood about the connection of these functionally relevant, collective movements with local atomic fluctuations, which are much faster. Here we show that pico- to nano-second timescale atomic fluctuations in hinge regions of adenylate kinase facilitate the large-scale, slower lid motions that produce a catalytically competent state. The fast, local mobilities differ between a mesophilic and hyperthermophilic adenylate kinase, but are strikingly similar at temperatures at which enzymatic activity and free energy of folding are matched. The connection between different timescales and the corresponding amplitudes of motions in adenylate kinase and their linkage to catalytic function is likely to be a general characteristic of protein energy landscapes.

1,011 citations