Fluid exit in reaction chambers

Abstract

Apparatus and methods are disclosed for controlling flow of fluid inside a chamber. A device comprises a chamber comprising at least one wall, a first opening for introducing a fluid into the interior of the chamber, and a second opening opposite the first opening. The at least one wall of the chamber is designed to provide a contracting section, a section having substantially constant cross-sectional area and a diffusing section through the chamber from the first opening to the second opening. The device may be employed as a gas outlet in a reaction chamber for conducting reactions where it is desired to control the internal atmosphere of the reaction chamber. The apparatus may be employed in the manufacture of biopolymers on the surface of a support such as an array of biopolymer features on the support. Also disclosed is a holding element for a support wherein the holding element is a low drag body.

1 . An apparatus for conducting chemical reactions wherein a plurality of drops of reagents are applied to the surface of a support in the form of an array, said apparatus comprising: 
 (a) a chamber,    (b) a gas inlet for introducing a gas into the interior of said chamber,    (c) a device for dispensing drops of reagents for conducting said chemical reactions in fluid communication with said chamber, and    (d) an opening in said chamber for exit of said gas, wherein said opening is designed to provide a contracting section, a section having substantially constant cross-sectional area and a diffusing section through said opening.    
     
     
         2 . An apparatus according to  claim 1  wherein contraction in said contracting section takes place over a region from about 0.15 to about 2 times the width of said section having substantially constant cross-sectional area.  
     
     
         3 . An apparatus according to  claim 1  wherein said diffusing section expands at a rate of about 0.08 to about 0.18 cm/cm.  
     
     
         4 . An apparatus for synthesizing a plurality of biopolymers on a support in the form of an array, said apparatus comprising: 
 (a) a chamber,    (b) a gas inlet for introducing a gas into the interior of said chamber,    (c) a device for dispensing reagents for synthesizing said biopolymers in the form of an array, said device being in fluid communication with said chamber, and    (d) an opening in said chamber for exit of said gas, wherein at least one wall of said opening is designed to provide a contracting section, a section having substantially constant cross-sectional area and a diffusing section through said opening.    
     
     
         5 . An apparatus according to  claim 4  wherein contraction in said contracting section takes place over a region from about 0.15 to about 2 times the width of said section having substantially constant cross-sectional area.  
     
     
         6 . An apparatus according to  claim 4  wherein said diffusing section expands at a rate of about 0.08 to about 0.18 cm/cm.  
     
     
         7 . An apparatus according to  claim 4  wherein said opening comprises a pair of side walls and both of said side walls of said pair are designed to provide a contracting section, a section of substantially constant cross-sectional area and a diffusing section through said opening.  
     
     
         8 . An apparatus according to  claim 4  further comprising a mechanism for moving said support into and out of said chamber and for positioning said support relative to said device for dispensing reagents.  
     
     
         9 . An apparatus according to  claim 8  further comprising a controller for controlling the movement of said mechanism for moving said support.  
     
     
         10 . An apparatus according to  claim 8  wherein said mechanism moves said support into and out of said chamber through said opening.  
     
     
         11 . An apparatus according to  claim 8  wherein said mechanism comprises a holding element for said support wherein said holding element is a low drag body having Reynolds numbers that are less than about 3000.  
     
     
         12 . An apparatus according to  claim 4  further comprising a manifold comprising at least two compartments, each of said compartments being in fluid communication with a respective gas inlet.  
     
     
         13 . An apparatus according to  claim 4  further comprising a mechanism for straightening the flow of a gas entering said gas inlet.  
     
     
         14 . An apparatus according to  claim 13  wherein said mechanism is a perforated element.  
     
     
         15 . An apparatus for synthesizing an array of biopolymers on a support, said apparatus comprising: 
 (a) a chamber,    (b) a gas inlet for introducing a gas into the interior of said chamber,    (c) a device for dispensing reagents for synthesizing said biopolymers, said device being in fluid communication with said chamber,    (d) an opening for exit of said gas, said opening comprising a pair of side walls, wherein at least one of said side walls is designed such that said opening comprises a contracting section, a section having substantially constant cross-sectional area and a diffusing section, wherein contraction in said contracting section takes place over a region from about 0.15 to about 2 times the width of said section having substantially constant cross-sectional area and wherein said diffusing section expands at a rate of about 0.08 to about 0.18 cm/cm and    (e) a mechanism for moving said support into and out of said chamber through said opening and for positioning said support relative to said device for dispensing reagents, wherein said mechanism comprises a holding element for said support wherein said holding element is a low drag body having Reynolds numbers that are less than about 3000.    
     
     
         16 . An apparatus according to  claim 15  wherein both of said side walls of said pair of side walls comprise a contracting section and a diffusing section.  
     
     
         17 . An apparatus according to  claim 15  further comprising a controller for controlling the movement of said mechanism for moving said support.  
     
     
         18 . An apparatus according to  claim 15  further comprising a manifold comprising at least two compartments, each of said compartments being in fluid communication with a respective gas inlet.  
     
     
         19 . An apparatus according to  claim 15  further comprising a mechanism for straightening the flow of a gas entering said gas inlet, said mechanism comprising a perforated element.  
     
     
         20 . A method for controlling the atmosphere in a reaction chamber, said method comprising: 
 (a) introducing a gas into said reaction chamber wherein said gas has a positive and substantially uniform unidirectional flow through said chamber and    (b) allowing said gas to exit said reaction chamber through a gas outlet in a direction that is the same as that of said unidirectional flow wherein in said gas outlet said gas flow is first contracted and then diffused.    
     
     
         21 . A method according to  claim 20  wherein said gas is contracted by a narrowing of at least one side wall in said gas outlet.  
     
     
         22 . A method according to  claim 21  wherein said narrowing takes place over a region from about 0.15 to about 2 times the width of said section having substantially constant cross-sectional area.  
     
     
         23 . A method according to  claim 20  wherein said gas is diffused by an expansion of at least one side wall in said gas outlet.  
     
     
         24 . A method according to  claim 23  wherein said expansion takes place over a region from about 2 to about 3 times the width of said section having substantially constant cross-sectional area.  
     
     
         25 . A method according to  claim 20  wherein said gas is contracted by a narrowing of opposing side walls in said gas outlet.  
     
     
         26 . A method according to  claim 20  wherein said gas is diffused by an expansion of opposing side walls in said gas outlet.  
     
     
         27 . A method for synthesizing a plurality of biopolymers on a support in the form of an array, said method comprising: 
 (a) introducing a support into a reaction chamber wherein said reaction chamber has a positive and substantially uniform unidirectional flow of gas therethrough wherein discrete sites on the surface of said support are activated and wherein said gas exits said reaction chamber through a gas outlet in a direction that is the same as said unidirectional flow wherein in said gas outlet said gas flow is first contracted and then diffused,    (b) bringing said support and a dispensing system for dispensing reagents for the synthesis of said biopolymers into a dispensing position relative to said activated discrete sites on said surface,    (c) dispensing said reagents to said discrete sites,    (d) removing said support and/or said dispensing system from said relative dispensing position, and    (e) optionally repeating steps (a) through (d) until said biopolymer is formed.    
     
     
         28 . A method according to  claim 27  wherein said gas is contracted by a narrowing of at least one side wall in said gas outlet.  
     
     
         29 . A method according to  claim 28  wherein said narrowing takes place over a region from about 0.15 to about 2 times the width of said section having substantially constant cross-sectional area.  
     
     
         30 . A method according to  claim 27  wherein said gas is diffused by an expansion of at least one side wall in said gas outlet.  
     
     
         31 . A method according to  claim 30  wherein said expansion takes place over a region from about 2 to about 3 times the width of said section having substantially constant cross-sectional area.  
     
     
         32 . A method according to  claim 27  wherein said gas is contracted by a narrowing of opposing side walls in said gas outlet.  
     
     
         33 . A method according to  claim 27  wherein said gas is diffused by an expansion of opposing side walls in said gas outlet.  
     
     
         34 . A method according to  claim 27  wherein said support is moved into and out of said chamber through said gas outlet.  
     
     
         35 . A method according to  claim 34  wherein said support is moved by a mechanism comprising a holding element for said support wherein said holding element is a low drag body having Reynolds numbers that are less than about 3000.  
     
     
         36 . A method according to  claim 27  wherein said gas is selected from the group consisting of nitrogen, argon, neon and helium.  
     
     
         37 . A method according to  claim 27  wherein said reagents are monomer addition reagents.  
     
     
         38 . A method according to  claim 27  wherein said biopolymers are polynucleotides or polypeptides.  
     
     
         39 . A method according to  claim 27  wherein said biopolymers are synthesized on said surface in multiple arrays and said support is subsequently diced into individual arrays of biopolymers on a support.  
     
     
         40 . A method according to  claim 27  for synthesizing an array of biopolymers on a surface of a support, said method comprising adding one or more polymer subunits at each of multiple feature locations on said support during each of multiple rounds of subunit additions wherein each round of subunit additions comprises: 
 (a) introducing said support into said reaction chamber,    (b) bringing said support and a dispensing system for dispensing said polymer subunits for the synthesis of said biopolymers into a dispensing position relative to said activated discrete sites on said surface,    (c) dispensing said polymer subunits to said discrete sites, and    (d) removing said support and/or said dispensing system from said relative dispensing position.    
     
     
         41 . A method according to  claim 27  wherein said biopolymers are synthesized on said surface in multiple arrays and said support is subsequently diced into individual arrays of biopolymers on a support.  
     
     
         42 . A method according to  claim 27  further comprising exposing the array to a sample and reading the array.  
     
     
         43 . A method according to  claim 42  comprising forwarding data representing a result obtained from a reading of the array.  
     
     
         44 . A method according to  claim 43  wherein the data is transmitted to a remote location.  
     
     
         45 . A method according to  claim 42  comprising receiving data representing a result of an interrogation obtained by the reading of the array.  
     
     
         46 . A device comprising: 
 (a) a mechanism for moving a support into and out of a chamber and for positioning said support relative to a device for dispensing reagents to a surface of said support to form an array of biopolymer features thereon, said mechanism comprising a holding element for said support wherein said holding element is a low drag body having Reynolds numbers that are less than about 3000, and    (b) a controller for controlling the movement of said mechanism for moving said support.