When microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory ({EGT).} We study the predictions of {EGT} for the bacterial “suicide bomber” game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters.

1 aAdami, Christoph1 aSchossau, Jory1 aHintze, Arend uhttp://link.aps.org/doi/10.1103/PhysRevE.85.01191400612nas a2200157 4500008004100000245010000041210006900141100001800210700001700228700001500245700002100260700001900281700002100300700001200321856012100333 2012 eng d00aExpression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis0 aExpression profiling of Cucumis sativus in response to infection1 aBuell, C., R.1 aAdhikari, B.1 aSavory, E.1 aVaillancourt, B.1 aChilds, K., L.1 aHamilton, J., P.1 aDay, B. uhttps://icer.msu.edu/research/publications/expression-profiling-cucumis-sativus-response-infection-pseudoperonospora00693nas a2200181 4500008004100000245011800041210006900159490000800228100001800236700002300254700002200277700001900299700001900318700002000337700001600357700001500373856012300388 2011 eng d00aEast African Food Security as Influenced by Future Climate Change and Land Use Change at Local to Regional Scales0 aEast African Food Security as Influenced by Future Climate Chang0 v1071 aMoore, Nathan1 aAlagarswamy, Gopal1 aPijanowski, Bryan1 aThornton, Phil1 aLofgren, Brent1 aOlson, Jennifer1 aYanda, Pius1 aQi, Jiaguo uhttps://icer.msu.edu/research/publications/east-african-food-security-influenced-future-climate-change-land-use-change00500nas a2200133 4500008004100000245006700041210006600108490000700174100002200181700001800203700002200221700001600243856010700259 2011 eng d00aEvaluating error propagation in coupled land-atmosphere models0 aEvaluating error propagation in coupled landatmosphere models0 v151 aPijanowski, Bryan1 aMoore, Nathan1 aMauree, Desaraden1 aNiyogi, Dev uhttps://icer.msu.edu/research/publications/evaluating-error-propagation-coupled-land-atmosphere-models01655nas a2200157 4500008004100000245010300041210006900144260001200213300001200225490000700237520107200244100001901316700002401335700001801359856012001377 2010 eng d00aEffect of membrane thickness on conformational sampling of phospholamban from computer simulations0 aEffect of membrane thickness on conformational sampling of phosp c03/2010 a805-8140 v983 aThe conformational sampling of monomeric, membrane-bound phospholamban is described from computer simulations. Phospholamban (PLB) plays a key role as a regulator of sarcoplasmic reticulum calcium ATPase. An implicit membrane model is used in conjunction with replica exchange molecular dynamics simulations to reach μs-ms timescales. The implicit membrane model was also used to study the effect of different membrane thicknesses by scaling the low-dielectric region. The conformational sampling with the membrane model mimicking dipalmitoylphosphatidylcholine bilayers is in good agreement overall with experimental measurements, but consists of a wide variety of different conformations including structures not described previously. The conformational ensemble shifts significantly in the presence of thinner or thicker membranes. This has implications for the structure and dynamics of PLB in physiological membranes and offers what we believe to be a new interpretation of previous experimental measurements of PLB in detergents and microsomal membrane.

1 aSayadi, Maryam1 aTanizaki, Seiichiro1 aFeig, Michael uhttps://icer.msu.edu/research/publications/effect-membrane-thickness-conformational-sampling-phospholamban-computer00498nas a2200109 4500008004100000245010800041210006900149490000800218100001700226700002000243856012500263 2010 eng d00aEquilibrium Molecular Dynamics Study of Lattice Thermal Conductivity/Conductance of Au-SAM-Au Junctions0 aEquilibrium Molecular Dynamics Study of Lattice Thermal Conducti0 v1321 aLuo, Tengfei1 aLloyd, John, R. uhttps://icer.msu.edu/research/publications/equilibrium-molecular-dynamics-study-lattice-thermal-conductivity-conductance00577nas a2200145 4500008004100000245010100041210006900142300001400211490000700225100002000232700001800252700002200270700001700292856012200309 2010 eng d00aEscherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects0 aEscherichia coli rpoB mutants have increased evolvability in pro a1338-13470 v271 aBarrick, J., E.1 aKauth, M., R.1 aStrelioff, C., C.1 aLenski, R.E. uhttps://icer.msu.edu/research/publications/escherichia-coli-rpob-mutants-have-increased-evolvability-proportion-their01895nas a2200217 4500008004100000245008800041210006900129260001200198490000700210520117900217653001901396653001701415653002801432653001901460653001501479653001401494653001301508100001801521700002001539856011801559 2009 eng d00aThe effective slip length and vortex formation in laminar flow over a rough surface0 aeffective slip length and vortex formation in laminar flow over c05/20090 v213 aThe flow of viscous incompressible fluid over a periodically corrugated surface is investigated numerically by solving the Navier–Stokes equation with the local slip and no-slip boundary conditions. We consider the effective slip length which is defined with respect to the level of the mean height of the surface roughness. With increasing corrugation amplitude the effective no-slip boundary plane is shifted toward the bulk of the fluid, which implies a negative effective slip length. The analysis of the wall shear stress indicates that a flow circulation is developed in the grooves of the rough surface provided that the local boundary condition is no-slip. By applying a local slip boundary condition, the center of the vortex is displaced toward the bottom of the grooves and the effective slip length increases. When the intrinsic slip length is larger than the corrugation amplitude, the flow streamlines near the surface are deformed to follow the boundary curvature, the vortex vanishes, and the effective slip length saturates to a constant value. Inertial effects promote vortex flow formation in the grooves and reduce the effective slip length.

10aexternal flows10alaminar flow10aNavier-Stokes equations10arough surfaces10ashear flow10aslip flow10avortices1 aNiavarani, A.1 aPriezjev, N., V uhttps://icer.msu.edu/research/publications/effective-slip-length-vortex-formation-laminar-flow-over-rough-surface00515nas a2200121 4500008004100000245009400041210006900135100001600204700002300220700001400243700001900257856011700276 2009 eng d00aEfficient Multi-label Ranking for Multi-class Learning: Application to Object Recognition0 aEfficient Multilabel Ranking for Multiclass Learning Application1 a.S.Bucak, S1 aMallapragada, P.K.1 aJin, Rong1 aJain, Anil, K. uhttps://icer.msu.edu/research/publications/efficient-multi-label-ranking-multi-class-learning-application-object00556nas a2200157 4500008004100000245007300041210006900114260001200183300001400195490000700209100001300216700002000229700002300249700002000272856010600292 2009 eng d00aElectronic structure of substitutional defects and vacancies in GaSe0 aElectronic structure of substitutional defects and vacancies in c02/2009 a344 - 3550 v701 aRak, Zs.1 aMahanti, S., D.1 aMandal, Krishna, C1 aFernelius, N.C. uhttps://icer.msu.edu/research/publications/electronic-structure-substitutional-defects-vacancies-gase00517nas a2200133 4500008004100000245008000041210006900121300001400190100001400204700001900218700001400237700001800251856011400269 2009 eng d00aEvolving coordinated quadruped gaits with the HyperNEAT generative encoding0 aEvolving coordinated quadruped gaits with the HyperNEAT generati a2764-27711 aClune, J.1 aBeckmann, B.E.1 aOfria, C.1 aPennock, R.T. uhttps://icer.msu.edu/research/publications/evolving-coordinated-quadruped-gaits-hyperneat-generative-encoding01687nas a2200145 4500008004100000245011000041210006900151260002800220520109700248100001901345700001701364700001901381700001601400856012501416 2009 eng d00aExperimental and Computational Analysis of Fuel Mixing in a Low Pressure Direct Injection Gasoline Engine0 aExperimental and Computational Analysis of Fuel Mixing in a Low aVail, Coloradoc07/20093 aAn experimental and computational investigation of the fuel spray mixing in an optically accessible single-cylinder direct-injection engine under realistic operating conditions was performed. High speed flow visualization in the op- tical engine was performed with images taken at a rate of 10,000 frames per second. The numerical simulations were carried out using the KIVA-3V software, which uses the discrete particle method for modeling the spray, with the secondary droplet breakup modeled by the Taylor Analogy Breakup (TAB) model. The nozzle configuration, jet orientation, injection flow rate and other injection parameters were matched with the experimental conditions. The simulated spray patterns in the cylinder were shown to compare well with the fuel distribution images obtained from the high speed flow visualization. The computational and experimental results for the fuel impingement on the cyl- inder walls, piston and valves, and those for the spark plug wetting and evaporated fuel mixing indicate the strong dependency of the fuel-air mixing to the spray pattern.

1 aSrivastava, S.1 aJaberi, F.A.1 aSchock, Harold1 aHung, David uhttps://icer.msu.edu/research/publications/experimental-computational-analysis-fuel-mixing-low-pressure-direct-injection01385nas a2200217 4500008004100000245007200041210006900113260001200182300001100194490000800205520071100213653002200924653002400946653001700970653003000987653000901017653002201026653001501048100002001063856008401083 2007 eng d00aEffect of surface roughness on rate-dependent slip in simple fluids0 aEffect of surface roughness on ratedependent slip in simple flui c10/2007 a1447080 v1273 aMolecular dynamics simulations are used to investigate the influence of molecular-scale surface roughness on the slip behavior in thin liquid films. The slip length increases almost linearly with the shear rate for atomically smooth rigid walls and incommensurate structures of the liquid/solid interface. The thermal fluctuations of the wall atoms lead to an effective surface roughness, which makes the slip length weakly dependent on the shear rate. With increasing the elastic stiffness of the wall, the surface roughness smoothes out and the strong rate dependence is restored again. Both periodically and randomly corrugated rigid surfaces reduce the slip length and its shear rate dependence.

10aelastic constants10ainterface roughness10aliquid films10amolecular dynamics method10aslip10asurface roughness10athin films1 aPriezjev, N., V uhttps://icer.msu.edu/effect-surface-roughness-rate-dependent-slip-simple-fluids01855nas a2200157 4500008004100000245017000041210006900211260001200280300001600292490000800308520120900316100001401525700001601539700001901555856012301574 2007 eng d00aExtension of the Renormalized Coupled-Cluster Methods Exploiting Left Eigenstates of the Similarity-Transformed Hamiltonian to Open- Shell Systems: A Benchmark Study0 aExtension of the Renormalized CoupledCluster Methods Exploiting c11/2007 a11359-113820 v1113 aThe recently formulated completely renormalized coupled-cluster method with singles, doubles, and noniterative triples, exploiting the biorthogonal form of the method of moments of coupled-cluster equations (Piecuch, P.; Włoch, M. J. Chem. Phys. 2005, 123, 224105; Piecuch, P.; Włoch, M.; Gour, J. R.; Kinal, A. Chem. Phys. Lett. 2006, 418, 467), termed CR-CC(2,3), is extended to open-shell systems. Test calculations for bond breaking in the OH radical and the ion and singlet−triplet gaps in the CH2, HHeH, and (HFH)- biradical systems indicate that the CR-CC(2,3) approach employing the restricted open-shell Hartree−Fock (ROHF) reference is significantly more accurate than the widely used CCSD(T) method and other noniterative triples coupled-cluster approximations without making the calculations substantially more expensive. A few molecular examples, including the activation energies of the C2H4 + H → C2H5 forward and reverse reactions and the triplet states of the CH2 and H2Si2O2 biradicals, are used to show that the dependence of the ROHF-based CR-CC(2,3) energies on the method of canonicalization of the ROHF orbitals is, for all practical purposes, negligible.

1 aWloch, M.1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/extension-renormalized-coupled-cluster-methods-exploiting-left-eigenstates-similarity-transformed01911nas a2200193 4500008004100000245014700041210006900188260001200257300001300269490000800282520117900290653003301469653001801502653002201520653002201542100001601564700001901580856011801599 2006 eng d00aEfficient Formulation and Computer Implementation of the Active-Space Electron-Attached and Ionized Equation-of-Motion Coupled-Cluster Methods0 aEfficient Formulation and Computer Implementation of the ActiveS c12/2006 a17 pages0 v1253 aThe efficient, general-purpose implementations of the active-space electron-attached (EA) and ionized (IP) equation-of-motion coupled-cluster (EOMCC) methods including up to 3p-2h and 3h-2p excitations, called EA-EOMCCSDt and IP-EOMCCSDt, respectively, are discussed. The details of the algorithm that enables one to achieve a high degree of code vectorization for the active-space methods and the factorized forms of the EA- and IP-EOMCCSDt equations that maximize the benefits of using active orbitals in the process of selecting the dominant 3p-2h and 3h-2p excitations are presented. The results of benchmark calculations for the low-lying doublet and quartet states of the CH and SH radicals reveal that the active-space EA-EOMCCSDt and IP-EOMCCSDt methods are capable of producing results for the electronic excitations in open-shell systems that match the high accuracy of EA- and IP-EOMCC calculations with a full treatment of 3p-2h and 3h-2p excitations, even when the excited states of interest display a manifestly multideterminantal nature, with the costs that can be on the same order of those characterizing the basic EOMCC singles and doubles approach.

10acoupled cluster calculations10afree radicals10aorganic compounds10asulphur compounds1 aGour, J., R1 aPiecuch, Piotr uhttps://icer.msu.edu/efficient-formulation-and-computer-implementation-active-space-electron-attached-and-ionized02232nas a2200253 4500008004100000245008800041210006900129260001100198300001400209490000800223520146400231100001901695700001601714700001401730700001701744700001501761700001801776700001401794700001701808700001401825700001801839700001501857856010601872 2006 eng d00aExperimental and Theoretical UV Characterizations of Acetyloacetone and its Isomers0 aExperimental and Theoretical UV Characterizations of Acetyloacet c2/2006 a3920-39260 v1103 aCryogenic matrix isolation experiments have allowed the measurement of the UV absorption spectra of the high-energy non-chelated isomers of acetylacetone, these isomers being produced by UV irradiation of the stable chelated form. Their identification has been done by coupling selective UV-induced isomerization, infrared spectroscopy, and harmonic vibrational frequency calculations using density functional theory. The relative energies of the chelated and non-chelated forms of acetylacetone in the S0 state have been obtained using density functional theory and coupled-cluster methods. For each isomer of acetylacetone, we have calculated the UV transition energies and dipole oscillator strengths using the excited-state coupled-cluster methods, including EOMCCSD (equation-of-motion coupled-cluster method with singles and doubles) and CR-EOMCCSD(T) (the completely renormalized EOMCC approach with singles, doubles, and non-iterative triples). For dipole-allowed transition energies, there is a very good agreement between experiment and theory. In particular, the CR-EOMCCSD(T) approach explains the blue shift in the electronic spectrum due to the formation of the non-chelated species after the UV irradiation of the chelated form of acetylacetone. Both experiment and CR-EOMCCSD(T) theory identify two among the seven non-chelated forms to be characterized by red-shifted UV transitions relative to the remaining five non-chelated isomers.

1 aPiecuch, Piotr1 aCoussan, S.1 aFerro, Y.1 aTrivella, A.1 aRoubin, P.1 aWieczorek, R.1 aManca, C.1 aKowalski, K.1 aWloch, M.1 aKucharski, S.1 aMusial, M. uhttps://icer.msu.edu/experimental-and-theoretical-uv-characterizations-acetyloacetone-and-its-isomers01765nas a2200169 4500008004100000245014000041210006900181260001100250300001400261490000800275520098500283653015801268100001901426700001601445700001401461856012001475 2006 eng d00aExtension of the Active-Space Equation-of- Motion Coupled-Cluster Methods to Radical Systems: The EA-EOMCCSDt and IPEOMCCSDt Approaches0 aExtension of the ActiveSpace Equationof Motion CoupledCluster Me c7/2006 a2854-28740 v1063 aThe development of the active-space variants of the electron-attached (EA) and ionized (IP) equation-of-motion coupled-cluster (EOMCC) methods, in which higher-than-doubly excited components of the cluster operator T and higher than 2p-1h or 2h-1p components of the electron attaching and ionizing operators R are defined through the use of active orbitals, is discussed. As shown by preliminary test calculations of adiabatic excitation energies and potential energy curves for the low-lying states of the CH and OH radicals, the basic active-space EA-EOMCC and IP-EOMCC methods, referred to as the EA-EOMCCSDt and IP-EOMCCSDt approaches, are capable of accuratelydescribing the ground and excited states of open-shell systems, even at the moderately stretched nuclear geometries and even for states with a strong multi-determinantal or doubly excited character, at the low costs that are on the order of those characterizing the standard EOMCC singles and doubles method.

10aoupled-cluster theory;equation-of-a motion coupled-cluster method;active-space coupled-cluster approaches;electronic-attached and ionized states;radicals1 aPiecuch, Piotr1 aGour, J., R1 aWloch, M. uhttps://icer.msu.edu/extension-active-space-equation-motion-coupled-cluster-methods-radical-systems-ea-eomccsdt-and00839nas a2200145 4500008004100000245009700041210006900138260001500207300001200222490000800234520030100242100002100543700001900564856011000583 2006 eng d00aExtrapolating Potential Energy Surfaces by Scaling Electron Correlation at a Single Geometry0 aExtrapolating Potential Energy Surfaces by Scaling Electron Corr c10/30/2006 a448-4530 v4303 aIt is shown that the molecular potential energy surface corresponding to a high level of ab initio theory can be accurately predicted by performing calculations with smaller basis sets and then scaling the electron correlation at a single point calculated with the larger target basis set.

1 aVarandas, A.J.C.1 aPiecuch, Piotr uhttps://icer.msu.edu/extrapolating-potential-energy-surfaces-scaling-electron-correlation-single-geometry01156nas a2200157 4500008004100000245012800041210006900169260001200238490000800250520055100258100001900809700001400828700001600842700001700858856012300875 2005 eng d00aExtension of Renormalized Coupled-Cluster Methods Including Triple Excitations to Electronic States of Open-Shell Molecules0 aExtension of Renormalized CoupledCluster Methods Including Tripl c06/20050 v1223 aThe general-purpose open-shell implementation of the completely renormalized equation-of-motion coupled-cluster approach with singles, doubles, and noniterative triples [CR-EOMCCSD(T)] is reported. Benchmark calculations for the low-lying doublet and quartet states of the CH radical show that the CR-EOMCCSD(T) method is capable of providing a highly accurate description of ground and excited states of open-shell molecules. This includes states with strong double excitation character, for which the conventional EOMCCSD approach fails.

1 aPiecuch, Piotr1 aWloch, M.1 aGour, J., R1 aKowalski, K. uhttps://icer.msu.edu/research/publications/extension-renormalized-coupled-cluster-methods-including-triple-excitations02334nas a2200133 4500008004100000245006900041210006800110260001500178490000800193520185400201100001902055700001702074856010902091 2005 eng d00aExtensive Generalization of Renormalized Coupled-Cluster Methods0 aExtensive Generalization of Renormalized CoupledCluster Methods c02/09/20050 v1223 aThe recently developed completely renormalized (CR) coupled-cluster (CC) methods with singles, doubles, and noniterative triples or triples and quadruples [CR-CCSD(T) or CR-CCSD(TQ), respectively], which are based on the method of moments of CC equations (MMCC) [K. Kowalski and P. Piecuch, J. Chem. Phys. 113, 18 (2000)], eliminate the failures of the standard CCSD(T) and CCSD(TQ) methods at larger internuclear separations, but they are not rigorously size extensive. Although the departure from strict size extensivity of the CR-CCSD(T) and CR-CCSD(TQ) methods is small, it is important to examine the possibility of formulating the improved CR-CC methods, which are as effective in breaking chemical bonds as the existing CR-CCSD(T) and CR-CCSD(TQ) approaches, which are as easy to use as the CR-CCSD(T) and CR-CCSD(TQ) methods, and which can be made rigorously size extensive. This may be particularly useful for the applications of CR-CC methods and other MMCC approaches in calculations of potential energy surfaces of large many-electron systems and van der Waals molecules, where the additive separability of energies in the noninteracting limit is very important. In this paper, we propose different types of CR-CC approximations, termed the locally renormalized (LR) CCSD(T) and CCSD(TQ) methods, which become rigorously size extensive if the orbitals are localized on nointeracting fragments. The LR-CCSD(T) and LR-CCSD(TQ) methods rely on the form of the energy expression in terms of the generalized moments of CC equations, derived in this work, termed the numerator-denominator-connected MMCC expansion. The size extensivity and excellent performance of the LR-CCSD(T) and LR-CCSD(TQ) methods are illustrated numerically by showing the results for the dimers of stretched HF and LiH molecules and bond breaking in HF and H2O.

1 aPiecuch, Piotr1 aKowalski, K. uhttps://icer.msu.edu/research/publications/extensive-generalization-renormalized-coupled-cluster-methods