SMDS

In the final step, the waxy heavy paraffin is catalytically hydrogenated, isomer-ized, and hydrocracked in a single trickle-bed reactor over a proprietary catalyst to 

Liquid fuel quality Poor (high S and aromatics) Excellent (low S and aromatics, high paraffin) 

Capital expense Slightly lower than ITCL 50K/bbl/day 

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Ahmad, S., Linnhoff, B., smd Smith, R., Cost Optimum Heat Exchanger Networks II. Targets and Design for Deteuled Capital Cost Models, Computers Chem. Eng., 14 751, 1990. 

Besides yielding qualitative information, these biologically and pharmaceutically motivated applications of SMD can also yield quantitative information about the binding potential of the ligand-receptor complex. A first advance in the reconstruction of the thermodynamic potential from SMD data by discounting irreversible work was made by Balsera et al. (1997) as outlined in Sect. Reconstruction of the potential of mean force below. 

An initial and desired final configuration of a system can be used by the targeted molecular dynamics (TMD) method (Schlitter et al., 1993) to establish a suitable pathway between the given configurations. The resulting pathway, can then be employed during further SMD simulations for choosing the direction of the applied force. TMD imposes time-dependent holonomic constraints which drive the system from one known state to another. This method is also discussed in the chapter by Helms and McCammon in this volume. 

The avidin-biotin complex, known for its extremely high affinity (Green, 1975), has been studied experimentally more extensively than most other protein-ligand systems. The adhesion forces between avidin and biotin have been measured directly by AFM experiments (Florin et al., 1994 Moy et al., 1994b Moy et al., 1994a). SMD simulations were performed on the entire tetramer of avidin with four biotins bound to investigate the microscopic detail of nnbinding of biotin from avidin (Izrailev et al., 1997). 

Phosphate release from actin. (a) Monomeric actin with ADP and Pi bound. The protein backbone (tube), ADP (grey spheres), and Ca -Pi (black spheres) are shown. The orientation of the spring indicates the pulling direction during P, unbinding. (b) Force exerted on the deprotonated (solid line) and protonated (dashed line) phosphate during the SMD simulations. 

Although extraction of lipids from membranes can be induced in atomic force apparatus (Leckband et al., 1994) and biomembrane force probe (Evans et al., 1991) experiments, spontaneous dissociation of a lipid from a membrane occurs very rarely because it involves an energy barrier of about 20 kcal/mol (Cevc and Marsh, 1987). However, lipids are known to be extracted from membranes by various enzymes. One such enzyme is phospholipase A2 (PLA2), which complexes with membrane surfaces, destabilizes a phospholipid, extracts it from the membrane, and catalyzes the hydrolysis reaction of the srir2-acyl chain of the lipid, producing lysophospholipids and fatty acids (Slotboom et al., 1982 Dennis, 1983 Jain et al., 1995). SMD simulations were employed to investigate the extraction of a lipid molecule from a DLPE monolayer by human synovial PLA2 (see Eig. 6b), and to compare this process to the extraction of a lipid from a lipid monolayer into the aqueous phase (Stepaniants et al., 1997). 

Another set of simulations was carried out with the targeted molecular dynamics (TMD) method (Schlitter et ah, 1993). The initial and final structures of an SMD simulation were used as input for the TMD simulations as discussed in Methods . TMD trajectories were calculated in both directions between the input structures, simulating both the binding and the... 

The SMD simulations were based on an NMR structure of the Ig domain 127 of the cardiac titin I-band (Improta et ah, 1996). The Ig domains consist of two /9-sheets packed against each other, with each sheet containing four strands, as shown in Fig. 8b. After 127 was solvated and equilibrated, SMD simulations were carried out by fixing one terminus of the domain and applying a force to the other in the direction from the fixed terminus to the other terminus. Simulations were performed as described by Eq. (1) with V = 0.5 A/ps and if = 10 ksT/A 414 pN/A. The force-extension profile from the SMD trajectory showed a single force peak as presented in Fig. 8a. This feature agrees well with the sawtooth-shaped force profile exhibited in AFM experiments. 

In this section we describe the behavior of a ligand subjected to three types of external forces a constant force, forces exerted by a moving stiff harmonic spring, and forces exerted by a soft harmonic spring. We then present a method of reconstruction of the potential of mean force from SMD force measurements employing a stiff spring (Izrailev et al., 1997 Balsera ct al., 1997). 

These examples illustrate that SMD simulations operate in a different regime than existing micromanipulation experiments. Considerably larger forces (800 pN vs. 155 pN) are required to induce rupture, and the scaling behavior of the drift regime, characterized by (9), differs qualitatively fi om the activated regime as characterized by (7). Hence, SMD simulations of rupture processes can not be scaled towards the experimental force and time scales. 

The rupture force measured in AFM experiments is given, therefore, by the average slope of the energy profile minus a correction related to the effects of thermal fluctuations. Equation (11) demonstrates that the rupture force measured in AFM experiments grows linearly with the activation energy of the system (Chilcotti et ah, 1995). A comparison of (10) and (11) shows that the unbinding induced by stiff springs in SMD simulations, and that induced by AFM differ drastically, and that the forces measured by both techniques cannot be readily related. 

The authors thank Y. Oono and M. Balsera for invaluable contributions to the joint development of SMD and J. Gullingsrud for many suggestions in the preparation of the manuscript. Images of molecular systems were produced with the program VMD (Humphrey et al., 1996). This work was supported by grants from the National Institute of Health (PHS 5 P41 RR05969-04), the National Science Foundation (BIR-9318159, BIR 94-23827 (EQ)), and the Roy J. Carver Charitable Trust. 

In our implementation of SMD, modified versions of VMD and Sigma communicate with each other using a customized, lightweight protocol. Sigma sends atomic positions resulting from each molecular dynamics time step to VMD for display. When the user specifies restraints on parts of the displayed model, VMD sends them to Sigma, where they are converted into potential-well restraints added to the force field [21]. 

Leech, J., Prins, J., Hermans, J. SMD Visual steering of molecular dynamics for protein design. IEEE Computational Science Engineering 3(4) (1996) 38-45... 

The first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

Description by rotational lists was introduced by Cook and Rohde [110] in the specification of the Standard Molecular Data (SMD) format [111]. In this stereochemical approach, the basic geometrical arrangements around a stcrcoccntcr arc defined in a list (c.g., square, tetrahedron, etc.). The atoms in those stcrcoclcmcnts are also labeled with numbers in a pre-defined way (Figure 2-72),... 

Thus, each stereochemical stnicttirc can be described and recognised with this rotational list if the structure is designated, c.g., in the STEREO block of the SMD format. The compact and extensible representation of the rotational list can include additional information, such as the name specification of the geometiy or whether the configuration is absohtte, relative, or racemic (Eigitre 2-73). 

Figure 2-73. The stereo part" (right) of a tetrahedral C-atom inciuded in the connection table of an SMD file.

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