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FieldAlign v2.0.1

FieldAlign v2.0.1 – 8.38 MB

FieldAlign™ is a smart molecular alignment tool for modellers and medicinal chemists. Given a 3D template molecule, it can align other molecules entered in 2D to that template rapidly and in a biologically-relevant manner. The template would commonly be an active molecule (or set of molecules) in its bioactive conformation. The template molecule could be obtained from a FieldTemplater™ alignment hypothesis, a ligand extracted from the active site of a protein, docking or pharmacophore studies.

FieldAlign v2.0.1

FieldAlign™ is ideal for visual inspection of alignments of actives from different series and identifying shared field features or pharmacophores, providing a qualitative indication of field SAR. FieldAlign is useful at the early stage of library design as small virtual libraries can be aligned to an active template and the chemist can select those scaffolds and monomers which together best match the active field template. FieldAlign can also be used as an aid to lead optimisation: iteratively changing molecules in FieldAlign and observing the alignments and field patterns can provide powerful insights into the direction that your chemistry should go. It is also invaluable for overlaying series of molecules prior to 3D QSAR studies where a good alignment of the molecules is critical for obtaining meaningful models.

FieldAlign™ is available as a Linux or Windows GUI program. A Linux command line version is also available which can be readily customized by expert users.

NEW FieldAlign v2.0 has been released! New features include
* Added the ability to add Field Constraints to any field point – force aligments to match specific field points!
* Added access to advanced options in the process dialog – change details of the conformation generation and alignment processes for optimum results
* Added the ability to save calculation settings for future use
* Added copy and paste from ChemDraw/ISISDraw
* Added import of conformation populations – align to your own sets of conformations
* Added the ability to log the calculation steps taken on each molecule and to view the log
* Added the ability to control the shape weighting in the scoring function
* Increased the number of database molecules that can be read into a single project to 500 (from 200)


Download: (Size: 8.38 MB)


From Research to Manuscript: A Guide to Scientific Writing

by Michael J. Katz

From Research to Manuscript, written in simple, straightforward language, explains how to understand and summarize a research project. It is a writing guide that goes beyond grammar and bibliographic formats, by demonstrating in detail how to compose the sections of a scientific paper. This book takes you from the data on your desk and leads you through the drafts and rewrites needed to build a thorough, clear science article. At each step, the book describes not only what to do but why and how. It discusses why each section of a science paper requires its particular form of information, and it shows how to put your data and your arguments into that form. Importantly, this writing manual recognizes that experiments in different disciplines need different presentations, and it is illustrated with examples from well-written papers on a wide variety of scientific subjects.

As a textbook or as an individual tutorial, From Research to Manuscript belongs in the library of every serious science writer and editor.


Schaum’s Outline of Heat Transfer

by Donald R. Pitts


The MIT Guide to Science and Engineering Communication

334 pages | PDF | 8,7 Mb
Drawing on their considerable experience teaching both college students and science professionals, James Paradis and Muriel Zimmerman have written a handbook that treats four kinds of literacy — written, oral, graphic, electronic — as crucial and inseparable to science and engineering communication.The MIT Guide emphasizes processes and forms that will help in creating documents and includes numerous realistic examples. A special feature of the book is its acceptance of the fact that most work in science these days is collaborative and that writing is often a group rather than a solitary activity. There is also a strong emphasis on the central role of the computer in creating and disseminating technical materials.First, Paradis and Zimmerman observe, it is essential to consider science and engineering as communication. The most effective engineers and scientists are skilled writers, and the first chapter shows how important good communication is to a successful career in science. The chapters that follow address such topics as: defining your audience and aims; organizing and drafting documents; revising for organization and style; developing graphics; conducting meetings; memos, letters, and e-mail; proposals; progress reports; reports and journal articles; instructional materials; electronic texts; oral presentations; job search strategies; document design for page and screen; strategies for searching the literature; and citation and reference styles.


Liquid Nitrogen Into A Swimming Pool

Chemical & Biomolecular Engineering

What is it like being a Chemical Engineer?

Feedback and Temperature Control

Differential Shell Momentum Balance in Rectangular Cartesian Coordinates

Transport Phenomena – Fluid Mechanics Theory

Differential Shell Momentum Balance in Rectangular Cartesian Coordinates

Preparation Just what you need to know !

A shell momentum balance is used below to derive a general differential equation that can be then employed to solve several fluid flow problems in rectangular Cartesian coordinates. For this purpose, consider an incompressible fluid in laminar flow under the effects of both pressure and gravity in a system of length L and width W, which is at an angle β to the vertical. End effects are neglected assuming the dimension of the system in the x-direction is relatively very small compared to those in the y-direction (W) and the z-direction (L).

figure : differential shell momentum balance in rectangular Cartesian coordinatesFigure. Differential rectangular slab (shell) of fluid of thickness Δx used in z-momentum balance for flow in rectangular Cartesian coordinates. The y-axis is pointing outward from the plane of the computer screen.

Since the fluid flow is in the z-direction, vx = 0, vy = 0, and only vz exists. For small flow rates, the viscous forces prevent continual acceleration of the fluid. So, vz is independent of z and it is meaningful to postulate that velocity vz = vz(x) and pressure p = p(z). The only nonvanishing components of the stress tensor are τxz = τzx, which depend only on x.

Consider now a thin rectangular slab (shell) perpendicular to the x-direction extending a distance W in the y-direction and a distance L in the z-direction. A ‘rate of z-momentum’ balance over this thin shell of thickness Δx in the fluid is of the form:

Rate of z-momentum           In − Out + Generation = Accumulation
At steady-state, the accumulation term is zero. Momentum can go ‘in’ and ‘out’ of the shell by both the convective and molecular mechanisms. Since vz(x) is the same at both ends of the system, the convective terms cancel out because (ρ vz vz W Δx)|z = 0 = (ρ vz vz W Δx)|z = L. Only the molecular term (L W τxz ) remains to be considered, whose ‘in’ and ‘out’ directions are taken in the positive direction of the x-axis. Generation of z-momentum occurs by the pressure force acting on the surface [p W Δx] and gravity force acting on the volume [(ρ g cos β) L W Δx].

The different contributions may be listed as follows:

  • rate of z-momentum in by viscous transfer across surface at x is (L W τxz )| x
  • rate of z-momentum out by viscous transfer across surface at x + Δx is (L W τxz )| x + Δx
  • rate of z-momentum in by overall bulk fluid motion across surface at z = 0 is (ρ vz vz W Δx )| z = 0
  • rate of z-momentum out by overall bulk fluid motion across surface at z = L is (ρ vz vz W Δx )| z = L
  • pressure force acting on surface at z = 0 is p0 W Δx
  • pressure force acting on surface at z = L is − pL W Δx
  • gravity force acting in z-direction on volume of rectangular slab is (ρ g cos β) L W Δx

On substituting these contributions into the z-momentum balance, we get

(L W τxz ) | x − (L W τxz ) | xx+ ( p 0p L ) W Δx + (ρ g cos β) L W Δx = 0

Dividing the equation by L W Δx yields

τxz | xxτxz | x


= p 0p L + ρ g L cos β



On taking the limit as Δx → 0, the left-hand side of the above equation is exactly the definition of the derivative. The right-hand side may be written in a compact and convenient way by introducing the modified pressure P, which is the sum of the pressure and gravitational terms. The general definition of the modified pressure is P  =  p + ρ g h , where h is the distance upward (in the direction opposed to gravity) from a reference plane of choice. The advantages of using the modified pressure P are that (i) the components of the gravity vector g need not be calculated; (ii) the solution holds for any flow orientation; and (iii) the fluid may flow as a result of a pressure difference, gravity or both. Here, h is negative since the z-axis points downward, giving h = − z cos β and therefore P  =  p − ρ g z cos β. Thus, P0  =  p0 at z = 0 and PL  =  pL − ρ g L cos β at z = L giving p0pL + ρ g L cos β  =  P0PL  ≡  ΔP. Thus, equation (2) yields



= ΔP



The first-order differential equation may be simply integrated to give

τxz  = ΔP


x + C1

Here, C1 is an integration constant, which is determined using an appropriate boundary condition based on the flow problem. Equation (4) shows that the momentum flux (or shear stress) distribution is linear in systems in rectangular Cartesian coordinates.Since equations (3) and (4) have been derived without making any assumption about the type of fluid, they are applicable to both Newtonian and non-Newtonian fluids. Some of the axial flow problems in rectangular Cartesian coordinates where these equations may be used as starting points are given below.

Related Problems in Transport Phenomena – Fluid Mechanics :

Transport Phenomena – Fluid Mechanics Problem : Newtonian fluid flow in plane narrow slit
– Determination of shear stress distribution, velocity profile and mass flow rate in slit flow for Newtonian fluid

Transport Phenomena – Fluid Mechanics Problem : Fluid flow in a falling film on an inclined flat surface
– Determination of shear stress distribution, velocity profile and film thickness in falling film

Transport Phenomena – Fluid Mechanics Problem : Power law fluid flow in plane narrow slit
– Determination of shear stress distribution, velocity profile and mass flow rate in slit flow for power law fluid

MIT Exam Problems on Fluid Mechanics, 1994-1998

Exam Problems on Fluid Mechanics, 1994-1998