Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Compaction simulator”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61Linked to original sources
PubMed1998

The solution structure of human coagulation factor VIIa in its complex with tissue factor is similar to free factor VIIa: a study of a heterodimeric receptor-ligand complex by X-ray and neutron scattering and computational modeling.

Factor VIIa (FVIIa) is a soluble four-domain plasma serine protease coagulation factor that forms a tight complex with the two extracellular domains of the transmembrane protein tissue factor in the initiating step of blood coagulation. To date, there is no crystal structure for free FVIIa. X-ray and neutron scattering data in solution for free FVIIa and the complex between FVIIa and soluble tissue factor (sTF) had been obtained for comparison with crystal structures of the FVIIa-sTF complex and of free factor IXa (FIXa). The solution structure of free FVIIa as derived from scattering data is consistent with the extended domain arrangement of FVIIa seen in the crystal structure of its complex with sTF, but is incompatible with the bent, less extended domain conformation seen in the FIXa crystal structure. The FVIIa scattering curve is also compatible with a subset of 317 possible extended structures derived from a constrained automated conformational search of 15 625 FVIIa domain models. Thus, the scattering data support extended domain models for FVIIa free in solution. Similar analyses showed that the solution scattering derived and crystal structures of the FVIIa-sTF complex were in good agreement. An automated constrained search for allowed structures for the complex in solution based on scattering curves showed that only a small family of compact models gave good agreement, namely those in which FVIIa and sTF interact closely over a large surface area. The general utility of this approach for structural analysis of heterodimeric complexes in solution is discussed. Analytical ultracentrifugation data and the modeling of these data were consistent with the scattering results. It is concluded that in solution FVIIa has an extended or elongated domain structure, which allows rapid interaction with sTF over a large surface area to form a high-affinity complex.

Amino Acid Sequence↗
PubMed2005

Focused fluid flow in passive continental margins.

Passive continental margins such as the Atlantic seaboard of Europe are important for society as they contain large energy resources, and they sustain ecosystems that are the basis for the commercial fish stock. The margin sediments are very dynamic environments. Fluids are expelled from compacting sediments, bottom water temperature changes cause gas hydrate systems to change their locations and occasionally large magmatic intrusions boil the pore water within the sedimentary basins, which is then expelled to the surface. The fluids that seep through the seabed at the tops of focused fluid flow systems have a crucial role for seabed ecology, and study of such fluid flow systems can also help in predicting the distribution of hydrocarbons in the subsurface and deciphering the climate record. Therefore, the study of focused fluid flow will become one of the most important fields in marine geology in the future.

Computer Simulation↗
PubMed2002

Transducer design for a portable ultrasound enhanced transdermal drug-delivery system.

For application in a portable transdermal drug-delivery system, novel transducers have been designed to enhance insulin transmission across skin using ultrasound. Previous research has shown transdermal delivery of insulin across skin using commercial sonicators operating at 20 kHz with intensities ranging from 12.5 to 225 mW/cm2. The goal of this research was to design and construct a small, lightweight transducer or array that could operate with a similar frequency and intensity range as a commercial sonicator used in previous transdermal ultrasound insulin experiments, but without the weight and mass of a sonicator probe. To obtain this intensity range, a cymbal transducer design was chosen because of its light, compact structure and low resonance frequency in water. To increase the spatial ultrasound field for drug delivery across skin, two arrays, each comprising of four cymbal transducers, were constructed. The first array, designated the standard array, used four cymbals transducer elements in parallel. A second array (named the stack array) used four cymbal transducers that used stacked piezoelectric discs to drive the titanium flextensional caps. Under similar driving conditions, the standard array produced intensities comparable to those achieved using a commercial sonicator.

Administration, Cutaneous↗
PubMed2000

Spontaneous speech recognition using a statistical coarticulatory model for the vocal-tract-resonance dynamics.

A statistical coarticulatory model is presented for spontaneous speech recognition, where knowledge of the dynamic, target-directed behavior in the vocal tract resonance is incorporated into the model design, training, and in likelihood computation. The principal advantage of the new model over the conventional HMM is the use of a compact, internal structure that parsimoniously represents long-span context dependence in the observable domain of speech acoustics without using additional, context-dependent model parameters. The new model is formulated mathematically as a constrained, nonstationary, and nonlinear dynamic system, for which a version of the generalized EM algorithm is developed and implemented for automatically learning the compact set of model parameters. A series of experiments for speech recognition and model synthesis using spontaneous speech data from the Switchboard corpus are reported. The promise of the new model is demonstrated by showing its consistently superior performance over a state-of-the-art benchmark HMM system under controlled experimental conditions. Experiments on model synthesis and analysis shed insight into the mechanism underlying such superiority in terms of the target-directed behavior and of the long-span context-dependence property, both inherent in the designed structure of the new dynamic model of speech.

Algorithms↗
PubMed1997

High-resolution solution structure of human pNR-2/pS2: a single trefoil motif protein.

pNR-2/pS2 is a 60 residue extracellular protein, which was originally discovered in human breast cancer cells, and subsequently found in other tumours and normal gastric epithelial cells. We have determined the three-dimensional solution structure of a C58S mutant of human pNR-2/pS2 using 639 distance and 137 torsion angle constraints obtained from analysis of multidimensional NMR spectra. A series of simulated annealing calculations resulted in the unambiguous determination of the protein's disulphide bonding pattern and produced a family of 19 structures consistent with the constraints. The peptide contains a single "trefoil" sequence motif, a region of about 40 residues with a characteristic sequence pattern, which has been found, either singly or as a repeat, in about a dozen extracellular proteins. The trefoil domain contains three disulphide bonds, whose 1-5, 2-4 and 3-6 cysteine pairings form the structure into three closely packed loops with only a small amount of secondary structure, which consists of a short alpha-helix packed against a two-stranded antiparallel beta-sheet. The structure of the domain is very similar to those of the two trefoil domains that occur in porcine spasmolytic polypeptide (PSP), the only member of the trefoil family whose three-dimensional structure has been previously determined. Outside the trefoil domain, which forms the compact "head" of the molecule, the N and C-terminal strands are closely associated, forming an extended "tail", which has some beta-sheet character for part of its length and which becomes more disordered towards the termini as indicated by (15)N{(1)H} NOEs. We have considered the structural implications of the possible formation of a native C58-C58 disulphide-bonded homodimer. Comparison of the surface features of pNR-2/pS2 and PSP, and consideration of the sequences of the other human trefoil domains in the light of these structures, illuminates the possible role of specific residues in ligand/receptor binding.

Amino Acid Sequence↗
PubMed2004

Computational modelling of final covers for uranium mill tailings impoundments.

To properly design a final cover for uranium mill tailings impoundments the designer must attempt to find an effective geotechnical solution which addresses the radiological and non-radiological potential impact and prevents geochemical processes from occurring within the tailings. This paper presents a computer-based method for evaluating the performance of engineered final covers for the remediation of uranium mill tailings impoundments. Three hypothetical final covers were taken from scientific literature to investigate the proposed method: (i) a compacted clay liner (CCL); (ii) a composite liner (CL) and (iii) a capillary barrier (CB). The processes investigated: (i) the saturated hydraulic flux; (ii) the unsaturated hydraulic flux (exclusively for the capillary barrier) and (iii) the radon exhalation to the atmosphere. The computer programs utilised for the analyses are: (i) Hydrologic Evaluation of Landfill Performance (HELP); (ii) SEEP/W and (iii) RADON. The site considered for the development of the research presented herein was the uranium mill tailings impoundment located at the Brazilian city of Poços de Caldas, in the Minas Gerais State.

Computer Simulation↗
PubMed2003

Interaction between the antigen and antibody is controlled by the constant domains: normal mode dynamics of the HEL-HyHEL-10 complex.

The antigen binding fragment (Fab) of a monoclonal antibody (HyHEL-10) consists of variable domains (Fv) and constant domains (CL-CH1). Normal modes have been calculated from the three-dimensional structures of hen egg lysozyme (HEL) with Fab, those of HEL with Fv, and so on. Only a small structural change was found between HEL-Fab and HEL-Fv complexes. However, HEL-Fv had a one order of magnitude lower dissociation constant than HEL-Fab. The Calpha fluctuations of HEL-Fab differed from those of HEL-Fv with normal mode calculation, and the dynamics can be thought to be related to the protein-protein interactions. CL-CH1 may have influence not only around local interfaces between CL-CH1 and Fv, but also around the interacting regions between HEL and Fv, which are longitudinally distant. Eighteen water molecules were found in HEL-Fv around the interface between HEL and Fv compared with one water molecule in HEL-Fab. These solvent molecules may occupy the holes and channels, which may occur due to imperfect complementarity of the complex. Therefore, the suppression of atomic vibration around the interface between Fv and HEL can be thought to be related to favorable and compact interface formation by complete desolvation. It is suggested that the ability to control the antigen-antibody affinity is obtained from modifying the CL-CH1. The second upper loop in the constant domain of the light chain (UL2-CL), which is a conserved gene in several light chains, showed the most remarkable fluctuation changes. UL2-CL could play an important role and could be attractive for modification in protein engineering.

Animals↗
PubMed2005

Structural investigations of DNA-polycation complexes.

The internal structure of DNA-polycation complexes is investigated by synchrotron small-angle X-ray scattering (SAXS). Hexagonal packing of DNA is observed for DNA complexed with poly-L-lysine (PL), poly-L-arginine (PA), spermine (Sp), and linear and branched polyethyleneimine (lPEI and bPEI, respectively). Variations in the internal spacings and degree of long-range ordering are dependent on both polycation type and concentration of added salt. With increasing concentration of monovalent salt, a discontinuous phase transition is observed from compact to loose bundles and finally to an isotropic network phase. This salt-induced melting transition was found to be universal for all polyplexes studied and is in quantitative agreement with a simple free energy model based solely on electrostatic and entropic contributions. Using the osmotic stress method, bulk modulus (K) is measured for PL-DNA and PA-DNA polyplexes at various salt concentrations. With increasing osmotic force, we show that the salt-induced melting transition is shifted and compression in the loose bundle regime is in qualitative agreement with our model.

Computer Simulation↗
PubMed2002

Distance and exposure dependent effective dielectric function.

In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (D(eff)) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of D(eff) versus the intercharge distance are in general sigmoidal with the characteristics of the curve depending on the distance of the two charges from the dielectric boundary and, secondarily, on the extent to which the area surrounding each charge is occupied by solvent (the "exposure"). The D(eff) values were fitted to an empirical, analytical function of these parameters that reproduces the data reasonably well, although considerable scatter exists in the range of D(eff) from 30 to 80. In the system used for parameterization, the mean square deviation of electrostatic interaction energies with this function is 0.48 kcal/mol, compared to 1.45 for an analytical Generalized Born model and 1.52 for the linear distance-dependent dielectric model. When tested in other proteins of varying size and compactness, the present function is superior to both of the above models, except for a fully unfolded polypeptide chain, where the Generalized Born model is superior.

Journal Article↗
PubMed2002

Blind deconvolution of ultrasound sequences using nonparametric local polynomial estimates of the pulse.

The problem of reconstructing the reflectivity of a biological tissue is examined by means of blind deconvolution of the echo ultrasound signals. It is shown that the quality of the reconstruction procedure can be significantly improved when initially the ultrasonic pulse is accurately estimated. A new approach to the estimation of the ultrasound pulse echo sequences is proposed, using local polynomial approximation, which is closely related to the wavelet transform theory. This approach can be viewed as a modification of homomorphic deconvolution, by using bases different from the Fourier basis of the space of square-integrable functions L2. The bases used here are the orthogonal compactly supported wavelet bases. It is shown that the locality of the estimate can be extremely useful in number of cases of practical interest, resulting in estimates with smaller root-mean squared (rms) errors, as compared with estimates employing the Fourier basis. This approach is applied to ultrasound signals, for estimation of the ultrasound pulse log-spectrum from the log-spectrum of radio-frequency (RF) sequences. It is shown, conceptually and experimentally, that the proposed approach can provide robust and rapidly computed estimates of the ultrasound pulses from the RF-sequences, as obtained in the process of tissue scanning. The pulse phase was recovered using the minimum-phase assumption, which was found to hold for the transducers in use. The obtained pulse estimates are used for the deconvolution of the RF-sequences, which result in stable estimates of the tissue reflectivity function, fairly independent of the properties of the imaging system. Simulated data, data obtained from several phantoms and from in vitro experiments have been processed and the results seem to be quite promising.

Animals↗
PubMed1998

Medial-point description of shape: a representation for action coding and its psychophysical correlates.

We describe a region-based shape representation that might be particularly useful from a biological perspective because it promotes the localization of objects, and object parts relative to each other. The proposed medial-point representation is similar to medial-axis type representations, but it is more compact. The medial points are those points along the medial axis that are equidistant from the longest segments of the boundary, therefore they represent the largest amount of edge information. The main advantage is that the original image can be reduced to a small number of points. We also provide psychophysical correlates of the representation for shapes with increasing complexity. Using a reverse mapping technique, we find that variations of contrast sensitivity within figures are defined by the shape of the bounding contour, and the peaks in the sensitivity maps correspond to the medial points of the proposed representation.

Computer Simulation↗
PubMed1994

Representations of metabolic knowledge: pathways.

The automatic generation of drawings of metabolic pathways is a challenging problem that depends intimately on exactly what information has been recorded for each pathway, and on how that information is encoded. The chief contributions of the paper are a minimized representation for biochemical pathways called the predecessor list, and inference procedures for converting the predecessor list into a pathway-graph representation that can serve as input to a pathway-drawing algorithm. The predecessor list has several advantages over the pathway graph, including its compactness and its lack of redundancy. The conversion between the two representations can be formulated as both a constraint-satisfaction problem and a logical inference problem, whose goal is to assign directions to reactions, and to determine which are the main chemical compounds in the reaction. We describe a set of production rules that solves this inference problem. We also present heuristics for inferring whether the exterior compounds that are substrates of reactions at the periphery of a pathway are side or main compounds. These techniques were evaluated on 18 metabolic pathways from the EcoCyc knowledge base.

Animals↗
PubMed1997

Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea.

Oxidized and reduced hen lysozyme denatured in 8 M urea at low pH have been studied in detail by NMR methods. 15N correlated NOESY and TOCSY experiments have provided near complete sequential assignment for both 1H and 15N resonances. Over 900 NOEs, including 130 (i, i + 2) and 23 (i, i + 3) NOEs, could be identified by analysis of the NOESY spectra of the denatured states, and 3J(HN, Halpha) coupling constants and 15N relaxation rates have been measured. The coupling constant and NOE data were analyzed by comparisons with theoretical predictions from a random coil polypeptide model based on amino acid specific phi,psi distributions extracted from the protein data bank. There is significant agreement between predicted and experimental NMR parameters suggesting that local conformations of the denatured states are largely determined by short-range interactions within the polypeptide chain. This result is supported by the observation that the chemical shift, coupling constant, and NOE data are little affected by whether or not the four disulfide bridge cross-links are formed in the denatured protein. The relaxation data, however, show significant differences between the oxidized and reduced protein. Analysis of the relaxation data in terms of simple dynamics models provides evidence for weak clustering of hydrophobic groups near tryptophan residues and increased barriers to motion in the more compact conformers formed when the polypeptide chain is cross-linked by the disulfide bridges. Using this information, a structural description of these denatured states is given in terms of an ensemble of conformers, which have a complex relationship between their local and global characteristics.

Amino Acid Sequence↗
PubMed1997

Effect of restricted conformational flexibility on the permeation of model hexapeptides across Caco-2 cell monolayers.

PURPOSE: To determine how restricted conformational flexibility of hexapeptides influences their cellular permeation characteristics. METHODS: Linear (Ac-Trp-Ala-Gly-Gly-X-Ala-NH2; X = Asp, Asn, Lys) and cyclic (cyclo[Trp-Ala-Gly-Gly-X-Ala]; X = Asp, Asn, Lys) hexapeptides were synthesized, and their transport characteristics were assessed using the Caco-2 cell culture model. The lipophilicities of the hexapeptides were determined using an immobilized artificial membrane. Diffusion coefficients used to calculate molecular radii were determined by NMR. Two-dimensional NMR spectroscopy, circular dichroism, and molecular dynamic simulations were used to elucidate the most favorable solution structure of the cyclic Asp-containing peptide. RESULTS: The cyclic hexapeptides used in this study were 2-3 times more able to permeate (e.g., Papp = 9.3 +/- 0.3 x 10(-8) cm/sec, X = Asp) the Caco-2 cell monolayer than were their linear analogs (e.g., Papp = 3.2 +/- 0.3 x 10(-8) cm/sec, X = Asp). In contrast to the linear hexapeptides, the flux of the cyclic hexapeptides was independent of charge. The cyclic hexapeptides were shown to be more lipophilic than the linear hexapeptides as determined by their retention times on an immobilized phospholipid column. Determination of molecular radii by two different techniques suggests little or no difference in size between the linear and cyclic hexapeptides. Spectroscopic data indicate that the Asp-containing linear hexapeptide exists in a dynamic equilibrium between random coil and beta-turn structures while the cyclic Asp-containing hexapeptide exists in a well-defined compact amphophilic structure containing two beta-turns. CONCLUSIONS: Cyclization of the linear hexapeptides increased their lipophilicities. The increased permeation characteristics of the cyclic hexapeptides as compared to their linear analogs appears to be due to an increase in their flux via the transcellular route because of these increased lipophilicities. Structural analyses of the cyclic Asp-containing hexapeptide suggest that its well-defined solution structure and, specifically the existence of two beta-turns, explain its greater lipophilicity.

Biological Transport↗
PubMed1997

Membrane time constant as a tool to assess cell degeneration.

Changes in neuronal surface area may be monitored by measuring the plasma membrane capacitance [8]. Membrane time constant (tao m) is given by the product of the membrane resistance (rm) and membrane capacitance (Cm), tao m = rm Cm. Thus, when membrane resistance is kept constant at a steady state (resting), membrane time constant can reflect the size of neuronal surface area. Membrane time constant is the time for the potential to fall from the resting to a fraction (1-l/e), or 63%, of its final value in the charging curve during the application of a small negative current pulse. Negative voltage shift from the resting potential hardly activates any voltage-dependent ion channel, resulting in nominal changes in cell membrane resistance. Although elaborated methods for mathematical models and simulations are available for the electrophysiological assessment of neuron geometry in order to estimate subthreshold potential attenuation during the propagation of synaptically mediated electrical signals, they involve a number of critical assumptions for the convenience to each model, and some of these assumptions are unlikely to be valid. With these restrictive assumptions, very little can be determined about the electronic structure of a neuron beyond the measurement of neuronal membrane resistance and membrane time constant. Alternatively, numerous tracers are available to visualize morphologies of neurons intracellularly and extracellularly. These anatomical methods provide direct and quantitative evidence for neuron geometry; however, they involve tissue processing and a series of chemical reactions, some of which are time- and effort-demanding. The purpose of the present paper is to show that membrane time constant can be effectively used as a tool to assess diminution in cell surface area without involving extensive mathematical theories and/or neuroanatomical techniques. This approach is particularly effective in electrotonically compact cells such as hippocampal neurons. Recent development in the technique of the whole-cell patch clamp recording in the slice preparation yielded longer time constant with better resolution due to the absence of the leak conductance associated with microelectrode impalement. Indeed, when membrane time constant was measured with the whole-cell patch clamp recording technique, it successfully detected the reduction in dendritic arbors (dendritic degeneration) in dentate granule cells in the pilocarpine model of chronic epilepsy, and this finding is supported by the neuroanatomical evidence that was obtained from the same specimen samples. Membrane time constant is an easy-to-measure "passive membrane property" and can be used as a reliable probe by itself for detecting dendritic degeneration or as a tool for decision-making in introducing neuroanatomical technique in combination with slice neurophysiology.

Animals↗
PubMed1991

The three-dimensional structure of a DNA hairpin in solution two-dimensional NMR studies and structural analysis of d(ATCCTATTTATAGGAT).

The hairpin formed by d(ATCCTATTTATAGGAT) was studied by means of two-dimensional NMR spectroscopy and conformational analysis. Almost all 1H resonances of the stem region could be assigned, while the 1H and 31P spectra of the loop region were interpreted completely; this includes the stereospecific assignment of the H5' and H5" resonances. The derivation of the detailed loop structure was carried out in a stepwise fashion including some improved and new methods for structure determination from NMR data. In the first step, the mononucleotide structures were examined. The conformational space available to the mononucleotide was scanned systematically by varying the glycosidic torsion angle and pseudorotational parameters. Each generated conformer was tested against the experimental J coupling constants and NOE parameters. In the following stage, the structures of dinucleotides and longer fragments were derived. Inter-residue distances between protons were calculated by means of a procedure in which the simulated NOEs, obtained via a relaxation-matrix approach, were fitted to the experimental NOEs without the introduction of a molecular model. In addition, the backbone torsion angles beta, gamma and epsilon were deduced from homocoupling and heterocoupling constants. These data served as constraints in the next step, in which the loop sequence was subjected to a multi-conformer generation procedure. The resulting structures were tested against the mentioned constraints and disregarded if these constraints were violated. This yielded a family of structures for the loop region, confined to a relatively narrow conformational space. A representative conformation was subsequently docked on a B-type stem which fulfilled the structural constraints (derived from the NMR experiments for the stem region) to yield the hairpin structure. Results obtained from subsequent restrained-molecular-mechanics as well as free-molecular-mechanics calculations are in accordance with those obtained by means of the analysis described above. The structure of the hairpin loop is a compactly folded conformation and the first base of the central TTTA region forms a Hoogsteen T-A pair with the fourth base. This Hoogsteen base pair is stacked upon the sixth base pair of the B-type double-helical stem. The second base of the loop is folded into the minor groove, whereas the third base of the loop is partly stacked on the first and fourth bases. The phosphate backbone exhibits a sharp turn between the third and fourth nucleotides of the loop. The peculiar structure of this hairpin loop is discussed in relation to loop folding in DNA and RNA hairpins and in relation to a general model for loop folding.

Base Sequence↗
PubMed2002

A novel silicon array designed for intraoperative charged particle imaging.

A novel Si-PIN imaging array is under investigation for a charged particle (beta, positron, or alpha) sensitive intraoperative camera to be used for (residual) tumor identification during surgery. This class of collimator-less nuclear imaging device has a higher signal response for direct interactions than its scintillator-optical detector-based counterparts. Monte Carlo simulations with 635 keV betas were performed, yielding maximum and projected ranges of 1.64 and 0.55 mm in Si. Up to 90% of these betas were completely absorbed in the first 0.30 mm. Based on these results, 300 microm thick prototype Si detector arrays were designed in a 16 x 16 crossed-grid arrangement with 0.8 mm wide orthogonal strips on 1.0 mm pitch. A NIM- and CAMAC-based high-density data acquisition and processing system was used to collect the list mode data. The system was calibrated by comparisons of measured spectra to energy deposition simulations or by direct measurement of various >100 keV conversion electron or beta emitters. Mean electronic noise per strip was <3.6 keV FWHM at room temperature. When detecting positrons, which have an accompanying 511 keV annihilation background, the flood irradiated beta/gamma ratio was approximately 40, indicating that beta images could be made without the use of background rejection techniques. The intrinsic spatial resolution corresponds to the 1 x 1 mm2 pixel size, and measurements of beta emitting point and line sources yielded FWHM resolutions of 1.5 (lateral) and 2.5 mm (diagonal), respectively, with the larger widths due to particle range blurting effects. Deconvolution of the finite source size yielded intrinsic resolutions that corresponded to the image pixel size. Transmission images of circle and line phantoms with various hole sizes and pitch were resolved with either pure beta or positron irradiation without a background correction. This novel semiconductor imaging device facilitates high charged particle and low gamma sensitivity, high signal/noise ratio, and allows for compact design to potentially aid surgical guidance by providing in situ images of clinical relevance.

Alpha Particles↗
PubMed2005

Molecular crowding enhances native state stability and refolding rates of globular proteins.

The presence of macromolecules in cells geometrically restricts the available space for poplypeptide chains. To study the effects of macromolecular crowding on folding thermodynamics and kinetics, we used an off-lattice model of the all-beta-sheet WW domain in the presence of large spherical particles whose interaction with the polypeptide chain is purely repulsive. At all volume fractions, phi(c), of the crowding agents the stability of the native state is enhanced. Remarkably, the refolding rates, which are larger than the value at phi(c) = 0, increase nonmonotonically as phi(c) increases, reaching a maximum at phi(c)=phi(c)(*). At high values of phi(c), the depletion-induced intramolecular attraction produces compact structures with considerable structure in the denatured state. Changes in native state stability and folding kinetics at phi(c) can be quantitatively mapped onto confinement in a volume-fraction-dependent spherical pore with radius R(s) approximately (4pi/3phi(c))(1/3) R(c) (R(c) is the radius of the crowding particles) as long as phi(c)< or =phi(c)(*). We show that the extent of native state stabilization at finite phi(c) is comparable with that in a spherical pore. In both situations, rate enhancement is due to destabilization of the denatured states with respect to phi(c) = 0.

Computer Simulation↗