Simulation vs. Understanding: A Tension,in Quantum Chemistry and Beyond. Part C. Toward Consilience

In the last part of our Essay, we outline a future of consilience, with a role both for fact‐seekers, and for searchers for understanding. We begin by looking at theory and simulation, surrounded as they are by and interacting with experiment, especially in Chemistry. Experimenters ask questions both conceptual and numerical, and so draw the communities together. Two case studies show what brings the theoretician authors joy in this playground, and two more detailed ones make it clear that computation/simulation is anyway deeply intertwined with theory‐building in what we do, or for that matter, anywhere in the profession. From a definition of science we try to foresee how simulation and theory will interact in the AI‐dominated future. We posit that Chemistry's streak of creation provides in that conjoined future a link to Art, and a passage to a renewed vision of the sacred in science.     

Simulation vs. Understanding: A Tension,in Quantum Chemistry and Beyond. Part A. Stage Setting

We begin our tripartite Essay with a triangle of understanding, theory and simulation. Sketching the intimate tie between explanation and teaching, we also point to the emotional impact of understanding. As we trace the development of theory in chemistry, Dirac's characterization of what is known and what is needed for theoretical chemistry comes up, as does the role of prediction, and Thom's phrase “To predict is not to explain.” We give a typology of models, and then describe, no doubt inadequately, machine learning and neural networks. In the second part, we leave philosophy, beginning by describing Roald's being beaten by simulation. This leads us to artificial intelligence (AI), Searle's Chinese room, and Strevens’ account of what a go-playing program knows. Back to our terrain—we ask “Quantum Chemistry, † ca. 2020?” Then move to examples of AI affecting social matters, ranging from trivial to scary. We argue that moral decisions are hardly to be left to a computer. At this point, we try to pull the reader up, giving the opposing view of an optimistic, limitless future a voice. But we don't do justice to that view—how could we? We return to questioning the ascetic dimension of scientists, their romance with black boxes. Onward: In the 3rd part of this Essay, we work our way up from pessimism. We trace (another triangle!) the special interests of experimentalists, who want the theory we love, and reliable numbers as well. We detail in our own science instances where theory gave us real joy. Two more examples-on magnetic coupling in inorganic diradicals, and the way to think about alkali metal halides, show us the way to integrate simulation with theory. Back and forth is how it should be—between painfully-obtained, intriguing numbers, begging for interpretation, in turn requiring new concepts, new models, new theoretically grounded tools of computation. Through such iterations understanding is formed. As our tripartite Essay ends, we outline a future of consilience, with a role both for fact-seekers, and searchers for understanding. Chemistry's streak of creation provides in that conjoined future a passage to art and to perceiving, as we argue we must, the sacred in science.     

Simulation vs. Understanding: A Tension,in Quantum Chemistry and Beyond. Part A. Stage Setting

We begin our tripartite Essay with a triangle of understanding, theory and simulation. Sketching the intimate tie between explanation and teaching, we also point to the emotional impact of understanding. As we trace the development of theory in chemistry, Dirac's characterization of what is known and what is needed for theoretical chemistry comes up, as does the role of prediction, and Thom's phrase “To predict is not to explain.” We give a typology of models, and then describe, no doubt inadequately, machine learning and neural networks. In the second part, we leave philosophy, beginning by describing Roald's being beaten by simulation. This leads us to artificial intelligence (AI), Searle's Chinese room, and Strevens’ account of what a go‐playing program knows. Back to our terrain—we ask “Quantum Chemistry, ? ca. 2020?” Then move to examples of AI affecting social matters, ranging from trivial to scary. We argue that moral decisions are hardly to be left to a computer. At this point, we try to pull the reader up, giving the opposing view of an optimistic, limitless future a voice. But we don't do justice to that view—how could we? We return to questioning the ascetic dimension of scientists, their romance with black boxes. Onward: In the 3rd part of this Essay, we work our way up from pessimism. We trace (another triangle!) the special interests of experimentalists, who want the theory we love, and reliable numbers as well. We detail in our own science instances where theory gave us real joy. Two more examples‐on magnetic coupling in inorganic diradicals, and the way to think about alkali metal halides, show us the way to integrate simulation with theory. Back and forth is how it should be—between painfully‐obtained, intriguing numbers, begging for interpretation, in turn requiring new concepts, new models, new theoretically grounded tools of computation. Through such iterations understanding is formed. As our tripartite Essay ends, we outline a future of consilience, with a role both for fact‐seekers, and searchers for understanding. Chemistry's streak of creation provides in that conjoined future a passage to art and to perceiving, as we argue we must, the sacred in science.     

Simulation vs. Understanding: A Tension,in Quantum Chemistry and Beyond. Part B. The March of Simulation,for Better or Worse

In the second part of this Essay, we leave philosophy, and begin by describing Roald's being trashed by simulation. This leads us to a general sketch of artificial intelligence (AI), Searle's Chinese room, and Strevens’ account of what a go-playing program knows. Back to our terrain—we ask “Quantum Chemistry, † ca. 2020?” Then we move to examples of Big Data, machine learning and neural networks in action, first in chemistry and then affecting social matters, trivial to scary. We argue that moral decisions are hardly to be left to a computer. And that posited causes, even if recognized as provisional, represent a much deeper level of understanding than correlations. At this point, we try to pull the reader up, giving voice to the opposing view of an optimistic, limitless future. But we don't do justice to that view—how could we, older mammals on the way to extinction that we are? We try. But then we return to fuss, questioning the ascetic dimension of scientists, their romance with black boxes. And argue for a science of many tongues.     

Simulation vs. Understanding: A Tension,in Quantum Chemistry and Beyond. Part B. The March of Simulation,for Better or Worse

In the second part of this Essay, we leave philosophy, and begin by describing Roald's being trashed by simulation. This leads us to a general sketch of artificial intelligence (AI), Searle's Chinese room, and Strevens’ account of what a go‐playing program knows. Back to our terrain—we ask “Quantum Chemistry, ? ca. 2020?” Then we move to examples of Big Data, machine learning and neural networks in action, first in chemistry and then affecting social matters, trivial to scary. We argue that moral decisions are hardly to be left to a computer. And that posited causes, even if recognized as provisional, represent a much deeper level of understanding than correlations. At this point, we try to pull the reader up, giving voice to the opposing view of an optimistic, limitless future. But we don't do justice to that view—how could we, older mammals on the way to extinction that we are? We try. But then we return to fuss, questioning the ascetic dimension of scientists, their romance with black boxes. And argue for a science of many tongues.     

Quantum chemistry simulation on quantum computers: theories and experiments

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.     

Computer modelling: Future directions

Summary Recent developments in computing and in the theory of simulation have extended greatly the successes of the modelling of ionic crystals pioneered by Mott and Littleton. This has changed the way in which computer experiments are brought to bear on an increasing range of solid-state phenomena. Yet applied science creates new demands, both in the form of new types of system and in terms of the complexity and subtlety of what is studied. The author's brief survey looks at some of the successes and gaps from interfaces and catalysts to neurotransmitters and from superconductors to slags.     

Analytical Chemistry,Past, Present and Future*This paper is dedicated to the Editorial Board of Analytical Letters.

ABSTRACT

Analytical Chemistry as a science has its own history as well as an important present and a sure future.

The aim of this paper is to demonstrate the role of Analytical Chemistry as a science and of Chemical Analysis as an art in the development of human society.

The correlation between method and instrument hyphenated by the sample is discussed along a long period of active Analytical Chemistry.

The connection between theory of Analytical Chemistry and the practice of chemical analysis enables us to be sure of the future of Analytical Chemistry.

We must consider that to do science it is necessary to know the history of science as well as to make research to be used not only in the present, but also in the near future.

Surely, Analytical Chemistry as a real scientific area will be on the top of sciences in the next century.     

The hydrogen bond

The concept of the hydrogen bond is a century old but remains youthful because of its vital role in so many branches of science and because of continued advances in experiment, theory and simulation. We discuss the structural and energetic characteristics of normal hydrogen bonds X–H···Y as well as some exceptions to the normal, including proton-shared and ion-pair bonds. We consider the harmonic and anharmonic vibration of X–H in a variety of complexes, and demonstrate that there is no fundamental difference between blue-shifting and red-shifting bonds. We discuss water clusters and liquid water and indicate possible directions of future progress.     

Quantum effects in biology

The idea that quantum-mechanical phenomena can play nontrivial roles in biology has fascinated researchers for a century. Here we review some examples of such effects, including light-harvesting in photosynthesis, vision, electron- and proton-tunneling, olfactory sensing, and magnetoreception. We examine how experimental tests have aided this field in recent years and discuss the importance of developing new experimental probes for future work. We examine areas that should be the focus of future studies and touch on questions such as biological relevance of quantum-mechanical processes. To exemplify current research directions, we provide some detailed discussions of quantum-coherence in photosynthetic light-harvesting and highlight the crucial interplay between experiment and theory that has provided leaps in our understanding. We address questions about why coherence matters, what it is, how it can be identified, and how we should think about optimization of light-harvesting and the role coherence plays.     

Recent Developments in Kramers’ Theory of Reaction Rates

In this short review, we provide an update of recent developments in Kramers’ theory of reaction rates. After a brief introduction stressing the importance of this theory initially developed for chemical reactions, we briefly present the main theoretical formalism starting from the generalized Langevin equation and continue by showing the main points of the modern Pollak, Grabert and Hänggi theory. Kramers’ theory is then sketched for quantum and classical surface diffusion. As an illustration the surface diffusion of Na atoms on a Cu(110) surface is discussed showing escape rates, jump distributions and diffusion coefficients as a function of reduced friction. Finally, some very recent applications of turnover theory to different fields such as nanoparticle levitation, microcavity polariton dynamics and simulation of reaction in liquids are presented. We end with several open problems and future challenges faced up by Kramers turnover theory.     

Opportunities and protocol for the teaching of materials science in africa

During the last 30 years the world's materials around us have changed from ‐ steel, concrete and wood to new materials with their own chemistry, and they constitute a large part of the manufacturing industry and our imports. Emphasis is on polymers, advanced materials for the electronic and medical industries and novel ceramics, amongst others. Yet, a school leaver often doesn't know much, or anything, about steel, concrete or what a plastic bag is and how to recycle it. There is an urgent need to address the improved teaching of materials science, especially in Africa [1, 2]. The NSF in America funded the Materials Science Department at Iowa University to create standards eight, nine and ten, i.e. senior high school, material science course. Sixteen teachers were used to write the notes and teachers manual. We are looking at the use of this course to promote materials science as a third matric science subject. We are of the opinion that this course could do much to improve science teaching in Africa and make the matric student much more conscious of materials around him/her. This presentation (which in some form had been presented at various conferences) mentions what this course in materials science and macromolecules covers and, further what we can do and achieve with multimedia education at university level [3, 4, 5, 6, 7, 8]. It will be based on the courses: MATTER, from Chapman‐Hall, developed by Liverpool University and Macrogalleria, developed by Prof. Lon Mathias at University of Southern Mississippi.     

Group contribution methods for molecular mixtures. III. Solution of groups tested via computer simulation

In this paper computer simulation results for model molecular fluids are used to test ideas underlying group contribution methods. The focus of attention is on the extent to which group contributions in one fluid (or two) can be used to estimate properties in other mixtures. This study is based on group—group distribution functions that were introduced in the first paper in this series.We propose two versions of an approach to a ”solution of groups“: a one-fluid theory and a two-fluid theory. The one-fluid theory subdivides into two forms and both result in group contributions to the residual internal energy that are independent of composition. The strong form of the one-fluid theory fails in comparisons with simulation data, but the weak form reliably predicts residual internal energies at low temperatures and low-to-moderate densities. The two-fluid version of the theory is somewhat better at estimating residual and excess internal energies.     

The effect of density on the properties of short chain fluids

We incorporate density dependence into continuum Born-Green-Yvon (BGY) theory through calculation of the end-to-end intramolecular correlation function. Whereas in previous studies we had only performed this calculation for the case of an isolated (zero-density) square-well chain of m segments (3相似文献   

Modeling molecular transport in slit pores

We examine the transport of methane in microporous carbon by performing equilibrium and nonequilibrium molecular dynamics simulations over a range of pore sizes, densities, and temperatures. We interpret these simulation results using two models of the transport process. At low densities, we consider a molecular flow model, in which intermolecular interactions are neglected, and find excellent agreement between transport diffusion coefficients determined from simulation, and those predicted by the model. Simulation results indicate that the model can be applied up to fluid densities of the order to 0.1-1 nm(-3). Above these densities, we consider a slip flow model, combining hydrodynamic theory with a slip condition at the solid-fluid interface. As the diffusion coefficient at low densities can be accurately determined by the molecular flow model, we also consider a model where the slip condition is supplied by the molecular flow model. We find that both density-dependent models provide a useful means of estimating the transport coefficient that compares well with simulation.     

Ultrafast internal conversion in ethylene. I. The excited state lifetime

Using a combined theoretical and experimental approach, we investigate the non-adiabatic dynamics of the prototypical ethylene (C(2)H(4)) molecule upon π → π? excitation. In this first part of a two part series, we focus on the lifetime of the excited electronic state. The femtosecond time-resolved photoelectron spectrum (TRPES) of ethylene is simulated based on our recent molecular dynamics simulation using the ab initio multiple spawning method with multi-state second order perturbation theory [H. Tao, B. G. Levine, and T. J. Martinez, J. Phys. Chem. A 113, 13656 (2009)]. We find excellent agreement between the TRPES calculation and the photoion signal observed in a pump-probe experiment using femtosecond vacuum ultraviolet (hν = 7.7 eV) pulses for both pump and probe. These results explain the apparent discrepancy over the excited state lifetime between theory and experiment that has existed for ten years, with experiments [e.g., P. Farmanara, V. Stert, and W. Radloff, Chem. Phys. Lett. 288, 518 (1998) and K. Kosma, S. A. Trushin, W. Fuss, and W. E. Schmid, J. Phys. Chem. A 112, 7514 (2008)] reporting much shorter lifetimes than predicted by theory. Investigation of the TRPES indicates that the fast decay of the photoion yield originates from both energetic and electronic factors, with the energetic factor playing a larger role in shaping the signal.     

The character of molecular modeling

In asking what progress might occur in molecular modeling in the next 25 years it is worth asking what progress has been made in the last twenty-five. In doing so it is hard to be optimistic for the future of the field unless a greater commitment is made to basic science.     

In silico prediction of drug solubility. 3. Free energy of solvation in pure amorphous matter

The solubility of drugs in water is investigated in a series of papers. In this work, we address the process of bringing a drug molecule from the vapor into a pure drug amorphous phase. This step enables us to actually calculate the solubility of amorphous drugs in water. In our general approach, we, on one hand, perform rigorous free energy simulations using a combination of the free energy perturbation and thermodynamic integration methods. On the other hand, we develop an approximate theory containing parameters that are easily accessible from conventional Monte Carlo simulations, thereby reducing the computation time significantly. In the theory for solvation, we assume that DeltaG* = DeltaGcav + ELJ + EC/2, where the free energy of cavity formation, DeltaGcav, in pure drug systems is obtained using a theory for hard-oblate spheroids, and ELJ and EC are the Lennard-Jones and Coulomb interaction energies between the chosen molecule and the others in the fluid. The theoretical predictions for the free energy of solvation in pure amorphous matter are in good agreement with free energy simulation data for 46 different drug molecules. These results together with our previous studies support our theoretical approach. By using our previous data for the free energy of hydration, we compute the total free energy change of bringing a molecule from the amorphous phase into water. We obtain good agreement between the theory and simulations. It should be noted that to obtain accurate results for the total process, high precision data are needed for the individual subprocesses. Finally, for eight different substances, we compare the experimental amorphous and crystalline solubility in water with the results obtained by the proposed theory with reasonable success.     

Monte Carlo simulation and molecular theory of tethered polyelectrolytes

We investigate the structure of end-tethered polyelectrolytes using Monte Carlo simulations and molecular theory. In the Monte Carlo calculations we explicitly take into account counterions and polymer configurations and calculate electrostatic interaction using Ewald summation. Rosenbluth biasing, distance biasing, and the use of a lattice are all used to speed up Monte Carlo calculation, enabling the efficient simulation of the polyelectrolyte layer. The molecular theory explicitly incorporates the chain conformations and the possibility of counterion condensation. Using both Monte Carlo simulation and theory, we examine the effect of grafting density, surface charge density, charge strength, and polymer chain length on the distribution of the polyelectrolyte monomers and counterions. For all grafting densities examined, a sharp decrease in brush height is observed in the strongly charged regime using both Monte Carlo simulation and theory. The decrease in layer thickness is due to counterion condensation within the layer. The height of the polymer layer increases slightly upon charging the grafting surface. The molecular theory describes the structure of the polyelectrolyte layer well in all the different regimes that we have studied.