Relative frequency function models for species distribution modeling

A new approach to habitat distribution modeling is presented and tested with data on North American plants. The relative frequency function (RFF) algorithm compares the relative frequencies of a species’ sample points to that of random points or absence points on the landscape to compute a frequency ratio. The relative frequency ratio r is smoothed across the range of values using moving, overlapping windows. The ratio of frequencies at a sample point for each variable is used to compute the geometric mean score for all data with non‐missing values. Variables are added using a forward stepwise method. Confidence intervals are computed with bootstrap resampling. The method was tested with artificial and species habitat and geographic range data. The RFF method in all cases gave results comparable to other methods tested. For the species with good geographic range maps, the results were consistent with known biogeography. The RFF method is particularly well‐suited to irregularly shaped distributions and can classify sample points even when the data contain missing values. The method is extremely simple to use and comes with a free software tool, does not require a large sample size, does not require absence data, and is more interpretable and portable than certain other methods.     

Recreational Fish-Finders—An Inexpensive Alternative to Scientific Echo-Sounders for Unravelling the Links between Marine Top Predators and Their Prey

Studies investigating how mobile marine predators respond to their prey are limited due to the challenging nature of the environment. While marine top predators are increasingly easy to study thanks to developments in bio-logging technology, typically there is scant information on the distribution and abundance of their prey, largely due to the specialised nature of acquiring this information. We explore the potential of using single-beam recreational fish-finders (RFF) to quantify relative forage fish abundance and draw inferences of the prey distribution at a fine spatial scale. We compared fish school characteristics as inferred from the RFF with that of a calibrated scientific split-beam echo-sounder (SES) by simultaneously operating both systems from the same vessel in Algoa Bay, South Africa. Customized open-source software was developed to extract fish school information from the echo returns of the RFF. For schools insonified by both systems, there was close correspondence between estimates of mean school depth (R² = 0.98) and school area (R² = 0.70). Estimates of relative school density (mean volume backscattering strength; S_v) measured by the RFF were negatively biased through saturation of this system given its smaller dynamic range. A correction factor applied to the RFF-derived density estimates improved the comparability between the two systems. Relative abundance estimates using all schools from both systems were congruent at scales from 0.5 km to 18 km with a strong positive linear trend in model fit estimates with increasing scale. Although absolute estimates of fish abundance cannot be derived from these systems, they are effective at describing prey school characteristics and have good potential for mapping forage fish distribution and relative abundance. Using such relatively inexpensive systems could greatly enhance our understanding of predator-prey interactions.     

A microcomputer-based video vector system for clinical gait analysis

A microcomputer-based video vector system has been developed to display the resultant ground reaction force vector on a television image of the subject in real-time. For each television field the force platform signals are acquired and processed and the resultant force vector superimposed on the video image of the walking subject. The force platform results are stored on disc and the composite video signals recorded on video tape for further analysis. The system is easy to set up and use and the results can be readily interpreted. The external moments produced at the joint centres by the ground reaction forces can be observed visually and, if required, quantification of the external moments can be achieved following data collection. The spatial resolution of the system is 0.342% vertically and 0.156% horizontally. The force vector visualization technique has routine applications in orthotics and prosthetics. It is also a useful technique for the teaching of biomechanics.     

Molecular dynamics simulation of hydrated Nafion with a reactive force field for water

We apply a newly parameterized central force field to highlight the problem of proton transport in fuel cell membranes and show that central force fields are potential candidates to describe chemical reactions on a classical level. After a short sketch of the parameterization of the force field, we validate the obtained force field for several properties of water. The experimental and simulated radial distribution functions are reproduced very accurately as a consequence of the applied parameterization procedure. Further properties, geometry, coordination, diffusion coefficient and density, are simulated adequately for our purposes. Afterwards we use the new force field for the molecular dynamics simulation of a swollen polyelectrolyte membrane similar to the widespread Nafion 117. We investigate the equilibrated structures, proton transfer, lifetimes of hydronium ions, the diffusion coefficients, and the conductivity in dependence of water content. In a short movie we demonstrate the ability of the obtained force field to describe the bond breaking/formation, and conclude that this force field can be considered as a kind of a reactive force field. The investigations of the lifetimes of hydronium ions give us the information about the kinetics of the proton transfer in a membrane with low water content. We found the evidence for the second order reaction. Finally, we demonstrate that the model is simple enough to handle the large systems sufficient to calculate the conductivity from molecular dynamics simulations. The detailed analysis of the conductivity reveals the importance of the collective moving of hydronium ions in membrane, which might give an interesting encouragement for further development of membranes. Figure: The structure of water in one pore of the highly hydrated Nafion membranes. Figure The structure of water in one of pore of the highly hydrated Nafion membrane Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Correlation between ground reaction force and tibial acceleration in vertical jumping

Modern electronics allow for the unobtrusive measurement of accelerations outside the laboratory using wireless sensor nodes. The ability to accurately measure joint accelerations under unrestricted conditions, and to correlate them with jump height and landing force, could provide important data to better understand joint mechanics subject to real-life conditions. This study investigates the correlation between peak vertical ground reaction forces, as measured by a force plate, and tibial axial accelerations during free vertical jumping. The jump heights calculated from force-plate data and accelerometer measurements are also compared. For six male subjects participating in this study, the average coefficient of determination between peak ground reaction force and peak tibial axial acceleration is found to be 0.81. The coefficient of determination between jump height calculated using force plate and accelerometer data is 0.88. Data show that the landing forces could be as high as 8 body weights of the jumper. The measured peak tibial accelerations ranged up to 42 g. Jump heights calculated from force plate and accelerometer sensors data differed by less than 2.5 cm. It is found that both impact accelerations and landing forces are only weakly correlated with jump height (the average coefficient of determination is 0.12). This study shows that unobtrusive accelerometers can be used to determine the ground reaction forces experienced in a jump landing. Whereas the device also permitted an accurate determination of jump height, there was no correlation between peak ground reaction force and jump height.     

A strategy for discovering biologically active compounds with high probability in traditional Chinese herb remedies: an application of saiboku-to in bronchial asthma.

A novel strategy for discovering biologically active components in traditional Chinese herb remedies was performed from a pharmacokinetic view. The hypothesis was that the active compounds should appear in blood and urine with appropriate blood concentrations and urinary excretion rates after the administration of herbal-extract mixtures. In this research, we applied our procedures to Saiboku-To, one of the most popular Chinese herbal medicines in Japan. Consisting of 10 different plant extracts, it is used for the treatment of bronchial asthma. The analytical method adopted was a rapid-flow fractionation (RFF) for extraction-fractionation of lipophilic components in urine followed by silica-gel high-performance liquid chromatography (HPLC) equipped with a multichannel ultraviolet (uv) absorption detector. beta-D-Glucuronidase-treated urine samples collected before and after the administration of Saiboku-To to healthy and asthmatic subjects were treated with the RFF apparatus to afford three pH-dependent fractions: strongly acidic (S), weakly acidic (W), and neutral (N). HPLC of these fractions, monitored by the multichannel uv detector, showed three new peaks in the postadministrative urine: one in the N fraction, two in the W fraction, and none in the S fraction. A compound in the N fraction was identified with authentic magnolol, a major component in Magnolia officinalis. Two compounds in the W fraction were identified by comparison with authentic samples as 8,9-dihydroxydihydromagnolol and liquiritigenin, metabolites previously isolated from M. officinalis and Glycyrrhiza glabra, respectively.     

细胞表面电荷的光镊测量方法及应用研究

分析了细胞表面电荷测量的意义、方法和现状,提出采用光镊技术测量细胞表面电荷的方法,介绍了实现该方法的系统构成和检测原理。在电场力的作用下,处于悬浮液中的带电细胞产生电泳。在外加电场力为零时利用激光的陷阱力捕获该细胞,然后施加并逐渐加大外加电场力,直到细胞刚好逃脱光阱力的束缚时的瞬间光阱力,理论上就是细胞所带电荷在电场中产生的库仑力与粘滞力之和。     

A method of calculating physiologically relevant joint reaction forces during forward dynamic simulations of movement from an existing knee model

In the commonly used SIMM software, which includes a complete musculoskeletal model of the lower limbs, the reaction forces at the knee are computed. These reaction forces represent the bone-on-bone contact forces and the soft tissue forces (e.g. ligaments) other than muscles acting at the joint. In the knee model integrated into this software, a patellotibial joint rather than a patellofemoral joint is defined, and a force acting along the direction of the patellar ligament is not included. Although this knee model results in valid kinematics and muscle moment arms, the reaction forces at the knee calculated do not represent physiologic knee joint reaction forces. Hence our objectives were to develop a method of calculating physiologic knee joint reaction forces using the knee model incorporated into the SIMM software and to demonstrate the differences in the forces returned by SIMM and the physiologic forces in an example. Our method converts the anatomically fictional patellotibial joint into a patellofemoral joint and computes the force in an inextensible patellar ligament. In our example, the rectus femoris was fully excited isometrically, with the knee and hip flexed to 90 degrees . The resulting SIMM tibiofemoral joint reaction force was primarily shear, because the quadriceps force was applied to the tibia via the fictional patellotibial joint. In contrast the physiologic tibiofemoral joint reaction force was primarily compression, because the quadriceps force was applied through the patellar ligament. This result illustrates that the physiologic knee joint reaction forces are profoundly different than the forces returned by SIMM. However physiologic knee joint reaction forces can be computed with postprocessing of SIMM results.     

Structural equilibrium of DNA represented with different force fields.

We have recently indicated preliminary evidence of different equilibrium average structures with the CHARMM and AMBER force fields in explicit solvent molecular dynamics simulations on the DNA duplex d(C5T5) . d(A5G5) (Feig, M. and B.M. Pettitt, 1997, Experiment vs. Force Fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B. (101:7361-7363). This paper presents a detailed comparison of DNA structure and dynamics for both force fields from extended simulation times of 10 ns each. Average structures display an A-DNA base geometry with the CHARMM force field and a base geometry that is intermediate between A- and B-DNA with the AMBER force field. The backbone assumes B form on both strands with the AMBER force field, while the CHARMM force field produces heterogeneous structures with the purine strand in A form and the pyrimidine strand in dynamical equilibrium between A and B conformations. The results compare well with experimental data for the cytosine/guanine part but fail to fully reproduce an overall B conformation in the thymine/adenine tract expected from crystallographic data, particularly with the CHARMM force field. Fluctuations between A and B conformations are observed on the nanosecond time scale in both simulations, particularly with the AMBER force field. Different dynamical behavior during the first 4 ns indicates that convergence times of several nanoseconds are necessary to fully establish a dynamical equilibrium in all structural quantities on the time scale of the simulations presented here.     

A molecular mechanical force field for the conformational analysis of oligosaccharides: comparison of theoretical and crystal structures of Man alpha 1-3Man beta 1-4GlcNAc

A molecular mechanical force field is described for the conformational analysis of oligosaccharides. This force field has been derived by the addition of new parameters to the AMBER force field and is compatible with simulations of proteins. This new parametrization is assessed by comparison of the theoretically predicted conformations of Man alpha 1-3Man beta 1-4GlcNAc with the corresponding crystal structure. Molecular dynamics simulation data are presented for this structure both in vacuo and with the explicit inclusion of water molecules. While the former demonstrate significant torsional oscillations about glycosidic linkages at physiological temperature, in the latter these oscillations are highly damped due to the stabilizing influence of a "cage" of solvent-solvent and solvent-solute hydrogen bonds.     

A novel high resolution Calpha--Calpha distance dependent force field based on a high quality decoy set

This work presents a novel C(alpha)--C(alpha) distance dependent force field which is successful in selecting native structures from an ensemble of high resolution near-native conformers. An enhanced and diverse protein set, along with an improved decoy generation technique, contributes to the effectiveness of this potential. High quality decoys were generated for 1489 nonhomologous proteins and used to train an optimization based linear programming formulation. The goal in developing a set of high resolution decoys was to develop a simple, distance-dependent force field that yields the native structure as the lowest energy structure and assigns higher energies to decoy structures that are quite similar as well as those that are less similar. The model also includes a set of physical constraints that were based on experimentally observed physical behavior of the amino acids. The force field was tested on two sets of test decoys not in the training set and was found to excel on all the metrics that are widely used to measure the effectiveness of a force field. The high resolution force field was successful in correctly identifying 113 native structures out of 150 test cases and the average rank obtained for this test was 1.87. All the high resolution structures (training and testing) used for this work are available online and can be downloaded from http://titan.princeton.edu/HRDecoys.     

Cell Membrane Tethers Generate Mechanical Force in Response to Electrical Stimulation

Living cells maintain a huge transmembrane electric field across their membranes. This electric field exerts a force on the membrane because the membrane surfaces are highly charged. We have measured electromechanical force generation by cell membranes using optically trapped beads to detach the plasma membrane from the cytoskeleton and form long thin cylinders (tethers). Hyperpolarizing potentials increased and depolarizing potentials decreased the force required to pull a tether. The membrane tether force in response to sinusoidal voltage signals was a function of holding potential, tether diameter, and tether length. Membrane electromechanical force production can occur at speeds exceeding those of ATP-based protein motors. By harnessing the energy in the transmembrane electric field, cell membranes may contribute to processes as diverse as outer hair cell electromotility, ion channel gating, and transport.     

All-atom and coarse-grained force fields for polydimethylsiloxane

By combining the bottom-up and top-down approaches, we have developed a new all-atom (AA) force field from quantum mechanics and experimental data and a new coarse grained (CG) force field from AA simulation and experimental data, for polydimethylsiloxane (PDMS). The AA force field is developed based on the TEAM force field database. The CG force field uses a mapping rule that splits the connecting oxygen into neighbouring CG beads to maintain the charge neutrality of the beads, analytical functional forms including anharmonic terms in the valence terms, and the temperature-dependent free-energy functional form to describe the inter-bead interactions. Broad range of thermodynamic properties of PDMS including density, surface tension, solubility parameter, radius of gyration and glass transition temperature are calculated to validate the force fields, and good agreements with the experimental data are obtained.     

Vibrational analysis of peptides,polypeptides, and proteins. II. β-Poly(L-alanine) and β-poly(L-alanylglycine)

The normal vibration frequencies of poly(L -alanine) and poly(L -alanylglycine) in the antiparallel chain-pleated sheet structure have been calculated, using the force field for polyglycine I from the previous paper (Biopolymers 15 , 2439–2464) plus additional force constants for the methyl group. The agreement with observed ir and Raman bands is very good. This substantiates the excellent transferability of the force field, since polyglycine I was shown to have a rippled-sheet structure. The amide I and amide II mode splittings are very well accounted for by transition dipole coupling, showing that subtle structural differences are sensitively manifested through this mechanism.     

A minimalist's reactive potential for efficient molecular modelling of chemistry

We review a minimalist's reactive force field, reactive state summation (RSS) potential. The essence of RSS potential scheme is to model each reactive state by individual non-reactive force fields, then modulate each term by a reaction-coordinate-dependent weight function, finally sum together to obtain the reactive potential. Compared with existing reactive potentials, RSS potential is easier to formulate and parameterise and is computationally efficient, at the expense of lesser accuracy. Thus, RSS potential can be regarded as a ‘reactive Lennard-Jones’ potential. Three exemplary RSS potentials are described in the context of their respective chemical systems: RSS-nitrogen for modelling detonation, RSS-carbon for modelling pyrolysis of activated carbon and RSS-fuel-catalyst for modelling catalytic chemical reaction.     

A new pairwise folding potential based on improved decoy generation and side-chain packing

A new force field for pairwise residue interactions as a function of C(alpha) to C(alpha) distances is presented. The force field was developed through the solution of a linear programming formulation with large sets of constraints. The constraints are based on the construction of >80,000 low-energy decoys for a set of proteins and requiring the decoy energies for each protein system to be higher than the native conformation of that particular protein. The generation of a robust force field was facilitated by the use of a novel decoy generation process, which involved the rational selection of proteins to add to the training set and included a significant energy minimization of the decoys. The force field was tested on a large set of decoys for various proteins not included in the training set and shown to perform well compared with a leading force field in identifying the native conformation for these proteins.     

A comparison of force fields for ethanol–water mixtures

Aqueous ethanol mixtures are studied through molecular dynamics simulations with the focus on exploring how various force field models reproduce the association and its influence on selected thermo-physical properties of these mixtures. The most important conclusion seems to be the inadequacy of all classical force fields to reproduce the very peculiar shape of the excess enthalpy of these mixtures, as a function of the ethanol concentration, neither quantitatively nor qualitatively. The Kirkwood–Buff (KB) integrals calculated using the simulation data follow the same trends as the experimental ones. This suggests complicated correlation of the excess enthalpy with the concentration fluctuation and clustering in these mixtures. The KB force field shows better overall agreement with experimental results than the other studied models.     

Association Kinetics from Single Molecule Force Spectroscopy Measurements

Single molecule force spectroscopy is often used to study the dissociation of single molecules by applying mechanical force to the intermolecular bond. These measurements provide the kinetic parameters of dissociation. We present what to our knowledge is a new atomic force microscopy-based approach to obtain the activation energy of the association reaction and approximate grafting density of reactive receptors using the dependence of the probability to form molecular bonds on probe velocity when one of the interacting molecules is tethered by a flexible polymeric linker to the atomic force microscopy probe. Possible errors in the activation energy measured with this approach are considered and resulting corrections are included in the data analysis. This new approach uses the same experimental setup as traditional force spectroscopy measurements that quantify dissociation kinetics. We apply the developed methodology to measure the activation energy of biotin-streptavidin association (including a contribution from the steric factor) and obtain a value of 8 ± 1 kT. This value is consistent with the association rate measured previously in solution. Comparison with the solution-derived activation energy indicates that kinetics of biotin-streptavidin binding is mainly controlled by the reaction step.